Physeter macrocephalus · seed P02185 · 154 aa · family defined as ≥30% identity to that seed · compiled 07 October 2026
Open in CODSWALLOP UniProt P02185 RCSB by accession PDBe-KB AlphaFold DB InterPro CATH 1.10.490.10 CATH 6.10.140.2100 CATH 6.10.140.2110 SCOP 8035604 SCOP 8043424 SCOP 8035773 SCOP 8061056 SCOP 8042926 RCSB 6CF0 PDBe
CATH and SCOP identifiers come from the RCSB's own structure annotations, which the Domains panel already reads, so these are looked up rather than guessed at.
Every figure here is counted over the whole family rather than quoted from one entry.
6CF0, the structure every other member of this family is superposed onto. Rendered by the RCSB and embedded here: the live app shows an interactive viewport, which a document that fetches nothing cannot.
How many of this family's constructs contain each residue of the seed. A trough is a stretch nobody has put in a construct, which is a construct-design answer rather than a disorder one.
180 distinct constructs across 561 entries. 530 polymer entities differ from the UniProt canonical sequence in some way, 14 carry a recognised expression tag and 0 carry a fusion partner.
"Differs from canonical" is not the same as "engineered". The canonical sequence is the full gene product, so a secreted protein whose structures all start after its signal peptide counts every one of them as different: lysozyme's most-used construct, residues 19–147 on 1,239 entities, is simply the mature protein. Read the construct column below for what was actually done, rather than this count.
| Entities | Length | Best (Å) | Best entry | What was made |
|---|---|---|---|---|
| 81 | 153 | 1.10 | 2EKT | residues 2-154 |
| 62 | 152 | 1.29 | 8BKN | residues 2-153 |
| 49 | 153 | 1.05 | 3VM9 | residues 2-154 |
| 26 | 154 | 1.30 | 1JW8 | D123N |
| 14 | 154 | 1.70 | 2SPL | L30F, D123N |
| 13 | 154 | 0.77 | 5YCE | matches the canonical sequence |
| 11 | 154 | 1.04 | 1NAZ | L30Y, H65Q, T68R +1 more |
| 11 | 154 | 1.70 | 5ILM | H65A, D123N |
| 8 | 154 | 1.76 | 8FB0 | H65Q, D123N |
| 6 | 146 | 0.91 | 3QM5 | matches the canonical sequence |
| 6 | 154 | 1.70 | 1MLL | V69F, D123N |
| 5 | 151 | 0.93 | 7VDN | residues 2-152 |
| 5 | 153 | 1.50 | 4MXL | residues 2-154; L30H, F44H, V69E |
| 5 | 153 | 1.68 | 2BW9 | residues 2-154; L30W, D123N |
| 5 | 154 | 1.50 | 1DO1 | L30W, D123N |
| 5 | 190 | 2.00 | 1URV | C38S, C83S |
| 4 | 153 | 1.37 | 3M3A | residues 2-154; L30H, F44H, V69E +1 more |
| 4 | 153 | 1.40 | 2EVK | residues 2-154; H94G |
| 4 | 153 | 1.70 | 1MWC | residues 2-154 |
| 4 | 153 | 1.80 | 1M6M | residues 2-154; V69N |
| 4 | 154 | 1.03 | 9T6Y | matches the canonical sequence |
| 4 | 154 | 1.45 | 1J3F | A72G |
| 4 | 154 | 1.45 | 8J4L | F47C |
| 4 | 154 | 1.70 | 1MTJ | F47V, D123N |
| 4 | 162 | 1.45 | 6F17 | His6; residues 2-154; H65V, V69A |
Showing the 25 most-used of 180.
Columns where the wild-type residue still dominates but a real minority carries something else, which is a different question from "what varies across species".
| Oligomeric state | Chains | Entries | Share |
|---|---|---|---|
| monomeric | 1 | 540 | 96.3% |
| dimeric | 2 | 17 | 3.0% |
| 20-meric | 20 | 1 | 0.2% |
| pentadecameric | 15 | 1 | 0.2% |
| decameric | 10 | 1 | 0.2% |
| hexameric | 6 | 1 | 0.2% |
293 entries have the depositor's assembly corroborated by PISA, 263 carry the depositor's word alone and 5 were assigned by PISA where the depositor gave none. The middle figure is not a disagreement: PISA may have returned nothing or never run. 5 entries carry more than one assembly with different chain counts, so they have no single answer to quote: 1JW8, 5KD1, 5VZO, 5VZP, 6E04.
Every source's own domains on the seed axis, one row each. They are not merged: Pfam, CATH, SCOP and InterPro disagree about boundaries, and a merged track would state a consensus none of them gave.
| Domain | Source | Span (seed) | Chains |
|---|---|---|---|
| Globins | CATH 1.10.490.10 | 2–154 | 427 |
| 6.10.140.2100 | CATH | 3–98 | 5 |
| 6.10.140.2110 | CATH | 99–154 | 5 |
| Globin-like | SCOP2B 8035604 | 2–152 | 354 |
| Globin-like | SCOP2B 8043424 | 3–154 | 140 |
| Globin-like | SCOP2B 8035773 | 3–154 | 16 |
| Globin-like | SCOP2B 8061056 | 8–152 | 5 |
| Globin-like | SCOP2B 8042926 | 20–154 | 8 |
HEM503 entries
NBN8 entries
FC65 entries
COH5 entries
HNN5 entries
EEE5 entries
ENC4 entries
MNR4 entries
PEO4 entries
J1S4 entries
J1R4 entries
CZM3 entries
| Component | Class | Name | Entries | Best (Å) |
|---|---|---|---|---|
| HEM | cofactor | Protoporphyrin Ix Containing Fe | 503 | 0.77 |
| SO4 | ion | Sulfate Ion | 386 | 0.77 |
| CMO | solvent | Carbon Monoxide | 146 | 0.93 |
| GOL | cryoprotectant | Glycerol | 36 | 1.09 |
| NO2 | ion | Nitrite Ion | 23 | 1.20 |
| OXY | solvent | Oxygen Molecule | 17 | 0.91 |
| IMD | buffer | Imidazole | 14 | 0.94 |
| EDO | cryoprotectant | 1,2-Ethanediol | 14 | 0.91 |
| CYN | ion | Cyanide Ion | 13 | 0.91 |
| NO | solvent | Nitric Oxide | 12 | 0.95 |
| OH | ion | Hydroxide Ion | 11 | 1.04 |
| PO4 | ion | Phosphate Ion | 10 | 1.45 |
| O | ion | Oxygen Atom | 9 | 1.05 |
| NBN | ligand | N-Butyl Isocyanide | 8 | 1.71 |
| XE | solvent | Xenon | 7 | 1.60 |
| CL | ion | Chloride Ion | 7 | 1.18 |
| NA | ion | Sodium Ion | 6 | 1.03 |
| AZI | ion | Azide Ion | 5 | 0.91 |
| FC6 | ligand | Hexacyanoferrate(3-) | 5 | 2.00 |
| COH | ligand | Protoporphyrin Ix Containing Co | 5 | 1.60 |
Parsed from the free text 432 depositors typed into
_exptl_crystal_grow.pdbx_details, out of 467
entries that recorded anything at all.
Median pH 7.4
(range 4.0 to 9.4).
561 entries carry a wwPDB validation report: 337 clean, 119 worth a check and 105 with something to explain. Median clashscore 5.93, median RSRZ outliers 1.32%, median R-free minus R-work 0.038. 510 have released structure factors.
| Organism | Entries | Best (Å) | Ligand-bound | Seed covered |
|---|---|---|---|---|
| Physeter macrocephalus | 360 | 0.77 | 359 | 100% |
| Equus caballus | 154 | 1.03 | 152 | 100% |
| Sus scrofa | 17 | 1.70 | 17 | 99% |
| Homo sapiens | 10 | 1.65 | 10 | 99% |
| Thunnus atlanticus | 9 | 0.91 | 9 | 96% |
| synthetic construct | 4 | 1.50 | 4 | 100% |
| Caretta caretta | 2 | 2.00 | 2 | 99% |
| Thunnus albacares | 1 | 1.74 | 1 | 96% |
| Elephas maximus | 1 | 1.78 | 1 | 99% |
| Kogia sima | 1 | 1.88 | 1 | 100% |
| Mirounga angustirostris | 1 | 1.90 | 1 | 100% |
| Phoca vitulina | 1 | 2.50 | 1 | 99% |
154 residues, numbered every ten. Every identity figure in this document is measured against this sequence.
active or binding site modified residue or glycosylation disulphide cysteine transmembrane or signal the 15 most-substituted positions
Sites are UniProt's curated features where the seed is a UniProt accession; the substituted positions are measured from this family's own alignment rather than annotated, and only the fifteen most substituted are marked: every position carrying a minority substitution would be most of the protein, because the family holds orthologues. A residue can carry more than one and is drawn with the first that applies, in the order of the key above.
One record per paper, not per entry.
| Year | Citation |
|---|---|
| 2026 | Coupled on-line in crystallo UV-Vis absorption spectroscopy and X-ray crystallography to compare specific radiation damage in metal-containing proteins at room versus cryogenic temperature. Acta Crystallogr D Struct Biol doi:10.1107/S2059798326000690 |
| 2026 | Computational design of generalist cyclopropanases with stereodivergent selectivity. Nat Commun doi:10.1038/s41467-026-68327-1 |
| 2026 | Myoglobin Amyloid Fibrils Reveal a Hierarchical Principle of Polymorphism and Electrostatic Self-Assembly. Nano Lett. doi:10.1021/acs.nanolett.6c02104 |
| 2025 | A Post-translational Histidine-Histidine Cross-Link Enhances Enzymatic Oxygen Reduction Activity with Greater pH Adaptability. J.Am.Chem.Soc. doi:10.1021/jacs.5c12710 |
| 2025 | Preliminary Serial Femtosecond Crystallography Studies of Myoglobin from Equine Skeletal Muscle Crystals doi:10.3390/cryst15100905 |
| 2024 | Biocatalytic strategy for the construction of sp 3 -rich polycyclic compounds from directed evolution and computational modelling. Nat.Chem. doi:10.1038/s41557-023-01435-3 |
| 2024 | Myoglobin-Catalyzed Azide Reduction Proceeds via an Anionic Metal Amide Intermediate. J.Am.Chem.Soc. doi:10.1021/jacs.3c09279 |
| 2024 | Influence of pump laser fluence on ultrafast myoglobin structural dynamics. Nature doi:10.1038/s41586-024-07032-9 |
| 2024 | Rational Design of an Artificial Metalloenzyme by Constructing a Metal-Binding Site Close to the Heme Cofactor in Myoglobin. Inorg.Chem. doi:10.1021/acs.inorgchem.4c03093 |
| 2024 | Redox Engineering of Myoglobin by Cofactor Substitution to Enhance Cyclopropanation Reactivity. Angew.Chem.Int.Ed.Engl. doi:10.1002/anie.202403485 |
| 2024 | Rational design of an artificial ethylbenzene hydroxylase using a molecular dynamics simulation to enhance enantioselectivity. Chem Lett. doi:10.1093/chemle/upad042 |
| 2024 | Improving Protein Expression, Stability, and Function with ProteinMPNN. J.Am.Chem.Soc. doi:10.1021/jacs.3c10941 |
| 2023 | Mechanistic manifold in a hemoprotein-catalyzed cyclopropanation reaction with diazoketone. Nat Commun doi:10.1038/s41467-023-43559-7 |
| 2023 | Tryptophan Can Promote Oxygen Reduction to Water in a Biosynthetic Model of Heme Copper Oxidases. Biochemistry doi:10.1021/acs.biochem.2c00300 |
| 2023 | Photocatalytic C-O Coupling Enzymes That Operate via Intramolecular Electron Transfer. J.Am.Chem.Soc. doi:10.1021/jacs.2c12226 |
| 2023 | Insights into Nitrosoalkane Binding to Myoglobin Provided by Crystallography of Wild-Type and Distal Pocket Mutant Derivatives. Biochemistry doi:10.1021/acs.biochem.2c00725 |
| 2023 | Crystal structural investigations of heme protein derivatives resulting from reactions of aryl- and alkylhydroxylamines with human hemoglobin. J.Inorg.Biochem. doi:10.1016/j.jinorgbio.2023.112304 |
| 2023 | Interactions of metronidazole and chloramphenicol with myoglobin: Crystal structure of a Mb-acetamide product. J Porphyr Phthalocyanines doi:10.1142/s1088424623500700 |
| 2022 | X-ray fluorescence holography of biological metal sites: Application to myoglobin. Biochem.Biophys.Res.Commun. doi:10.1016/j.bbrc.2022.10.003 |
| 2022 | Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization. Biochemistry doi:10.1021/acs.biochem.2c00033 |
| 2022 | NMR-guided directed evolution. Nature doi:10.1038/s41586-022-05278-9 |
| 2021 | Experimental and theoretical study on converting myoglobin into a stable domain-swapped dimer by utilizing a tight hydrogen bond network at the hinge region. Rsc Adv doi:10.1039/d1ra06888a |
| 2021 | An Engineered Glutamate in Biosynthetic Models of Heme-Copper Oxidases Drives Complete Product Selectivity by Tuning the Hydrogen-Bonding Network. Biochemistry doi:10.1021/acs.biochem.0c00852 |
| 2021 | Noncanonical Heme Ligands Steer Carbene Transfer Reactivity in an Artificial Metalloenzyme*. Angew.Chem.Int.Ed.Engl. doi:10.1002/anie.202103437 |
| 2021 | Common and unique strategies of myoglobin evolution for deep-sea adaptation of diving mammals. Iscience doi:10.1016/j.isci.2021.102920 |
| 2021 | Rational design of metal-binding sites in domain-swapped myoglobin dimers. J.Inorg.Biochem. doi:10.1016/j.jinorgbio.2021.111374 |
| 2021 | Serial femtosecond and serial synchrotron crystallography can yield data of equivalent quality: A systematic comparison. Sci Adv doi:10.1126/sciadv.abf1380 |
| 2020 | Thermodynamic Control of Domain Swapping by Modulating the Helical Propensity in the Hinge Region of Myoglobin. Chem Asian J doi:10.1002/asia.202000307 |
| 2020 | A Catalytic Binding Site Together with a Distal Tyr in MyoglobinAffords Catalytic Efficiencies Similar to Natural Peroxidases. Acs Catalysis doi:10.1021/acscatal.9b05080 |
| 2019 | Origin of high stereocontrol in olefin cyclopropanation catalyzed by an engineered carbene transferase. Acs Catalysis doi:10.1021/acscatal.8b04073 |
| 2019 | Anisotropic Distribution of Ammonium Sulfate Ions in Protein Crystallization Cryst.Growth Des. doi:10.1021/acs.cgd.9b00256 |
| 2019 | Fixed-target serial oscillation crystallography at room temperature. IUCrJ doi:10.1107/S2052252519001453 |
| 2019 | Unique Tyr-heme double cross-links in F43Y/T67R myoglobin: an artificial enzyme with a peroxidase activity comparable to that of native peroxidases. Chem.Commun.(Camb.) doi:10.1039/c9cc02714a |
| 2018 | Tracing whale myoglobin evolution by resurrecting ancient proteins. Sci Rep doi:10.1038/s41598-018-34984-6 |
| 2018 | A Noncanonical Proximal Heme Ligand Affords an Efficient Peroxidase in a Globin Fold. J. Am. Chem. Soc. doi:10.1021/jacs.7b12621 |
| 2018 | Capture and characterization of a reactive haem-carbenoid complex in an artificial metalloenzyme Nat Catal doi:10.1038/s41929-018-0105-6 |
| 2018 | A Rationally Designed Myoglobin Exhibits a Catalytic Dehalogenation Efficiency More than 1000-Fold That of a Native Dehaloperoxidase Acs Catalysis doi:10.1021/acscatal.8b02979 |
| 2018 | Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets. Biochemistry doi:10.1021/acs.biochem.8b00542 |
| 2018 | Formation of Cys-heme cross-link in K42C myoglobin under reductive conditions with molecular oxygen J. Inorg. Biochem. doi:10.1016/j.jinorgbio.2018.02.011 |
| 2018 | Regulation of both the structure and function by a de novo designed disulfide bond: a case study of heme proteins in myoglobin Chem. Commun. (Camb.) doi:10.1039/c8cc01646a |