CODSWALLOP

LYSOZYME

Gallus gallus · seed 1AKI_1 · 129 aa · family defined as ≥30% identity to that seed · compiled 09 August 2026

1,687Entries
1,688Polymer entities
281Distinct constructs
26Organisms
324Ligand-bound
0.65 ÅBest resolution
1.74 ÅMedian resolution

Every figure here is counted over the whole family rather than quoted from one entry.

Constructs, most-used first

281 distinct constructs across 1,687 entries. 1,607 polymer entities differ from the UniProt canonical sequence in some way, 1 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.

EntitiesLengthBest (Å)Best entryWhat was made
1239 129 0.65 2VB1 residues 19-147
64 147 0.83 9QUM matches the canonical sequence
36 130 1.04 2NWD residues 19-148
12 123 1.90 1YRO residues 21-143
12 129 1.12 1JSE residues 19-147
7 129 1.60 1LMQ residues 16-144; A101D
6 128 0.98 5HMV residues 19-146
5 123 1.85 6IP9 residues 20-142
5 127 1.20 6F9Y residues 19-145
4 130 0.89 7P6M residues 18-147
4 130 1.80 1HNL residues 19-148; C95A
3 129 1.11 5V92 residues 19-147; N84D, P97R, S118R +1 more
3 129 1.90 1DKK matches the canonical sequence
2 121 1.20 7EKA residues 20-140
2 122 1.90 2FBD residues 20-141
2 125 2.29 9J0L residues 23-147
2 127 1.76 1UIA residues 19-147; 1 internal deletion
2 129 1.39 7YNV residues 19-147; A49V
2 129 1.56 3WVY residues 19-147; D66A
2 129 1.64 1H6M residues 19-147; E53Q
2 129 1.80 1LZD residues 19-147; W80Y
2 129 1.90 3A3R residues 19-147; N77D
2 129 1.90 5VJQ no UniProt reference for this entity, so it cannot be diffed against a canonical sequence
2 130 1.70 1TCY residues 19-148; Y81F
2 130 1.77 1TBY residues 19-148; Y81L

Showing the 25 most-used of 281.

Positions people deliberately mutate

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".

Q121R 18% S91A 17% R73V 17% A122Q 17% G4E 17% F34W 17% S85Q 17% A90D 17% N93A 17% L75A 17% A31L 16% R68K 16% A10R 16% M12L 16% N19G 16% L56F 16% P79S 16% S86D 16% G26A 16% N37G 16% T118R 16% R128G 16% H15L 16% W62Y 16% N103Q 16% M105I 16% Y23I 16% F38Y 16% T47A 16% N106R 16%

What it assembles into

Oligomeric stateChainsEntriesShare
monomeric1 1,532 90.8%
dimeric2 72 4.3%
trimeric3 67 4.0%
tetrameric4 3 0.2%
heptameric7 3 0.2%
hexameric6 1 0.1%
pentameric5 1 0.1%
24-meric24 1 0.1%

883 entries have the depositor's assembly corroborated by PISA, 759 carry the depositor's word alone and 45 were assigned by PISA where the depositor gave none. The middle figure is not a disagreement: PISA may have returned nothing or never run. 19 entries carry more than one assembly with different chain counts, so they have no single answer to quote: 1ZMY, 2FBD, 2HU1, 2HU3, 3F6Z, 3LN2, 3P66, 3TMU, 3TMV, 3TMW, 3TMX, 3WU7, 3WU8, 3WU9, 3WUA, 4LYB, 4LYC, 4PHI, 5KKI.

Domain architecture

DomainSourceSpan (seed)Chains
1.10.530.10CATH 1–129 1,288
Lysozyme-likeSCOP2B 8037428 1–129 1,271
Lysozyme-likeSCOP2B 8043304 1–129 211

What binds it

ComponentClassNameEntriesBest (Å)
NAion Sodium Ion 865 0.80
CLion Chloride Ion 773 0.80
EDOcryoprotectant 1,2-Ethanediol 145 0.65
ACTcryoprotectant Acetate Ion 144 0.65
GOLcryoprotectant Glycerol 121 1.05
NO3ion Nitrate Ion 109 0.65
DMScryoprotectant Dimethyl Sulfoxide 64 0.98
PTion Platinum (Ii) Ion 37 0.98
CAion Calcium Ion 35 1.15
NDGcofactor 2-Acetamido-2-Deoxy-Alpha-D-Glucopyranose 31 1.45
SO4ion Sulfate Ion 30 1.13
RUion Ruthenium Ion 27 0.98
EPEbuffer 4-(2-Hydroxyethyl)-1-Piperazine Ethanesulfonic Acid 20 0.94
BRion Bromide Ion 18 1.03
CPTligand Cisplatin 18 0.98
AUion Gold Ion 17 1.10
DO3ligand 10-((2r)-2-Hydroxypropyl)-1,4,7,10-Tetraazacyclododecane 1,4,7-T 16 0.80
GDion Gadolinium Atom 16 0.80
IODion Iodide Ion 15 1.10
QPTligand Carboplatin 15 1.60

How it crystallises

Parsed from the free text 1,414 depositors typed into _exptl_crystal_grow.pdbx_details, out of 1,505 entries that recorded anything at all. Median pH 4.6 (range 3.0 to 10.0).

Precipitants

Sodium chloride × PEG × Ammonium sulfate × Sodium citrate × MPD × Sodium formate × Calcium chloride × Magnesium chloride × Lithium sulfate × Ethanol × Ammonium phosphate × Isopropanol × Dioxane × Jeffamine ×

Buffers

Sodium acetate × Phosphate × Citrate × HEPES × Tris × MES × Imidazole × Sodium cacodylate × Bis-Tris × Bis-Tris propane × Glycine × CHES ×

Which entries to trust

1,686 entries carry a wwPDB validation report: 1,101 clean, 424 worth a check and 161 with something to explain. Median clashscore 5.01, median RSRZ outliers 1.55%, median R-free minus R-work 0.036. 1,450 have released structure factors.

Across species

OrganismEntriesBest (Å)Ligand-boundSeed covered
Gallus gallus1,378 0.65 301 100%
Homo sapiens219 1.06 5 100%
Mus musculus14 1.90 12 98%
Meleagris gallopavo13 1.12 1 100%
Bos taurus9 1.20 1 100%
Anas platyrhynchos7 1.11 0 100%
Oncorhynchus mykiss7 1.60 3 98%
Capra hircus5 1.60 0 93%
Canis lupus familiaris5 1.85 0 100%
Asplenium bulbiferum subsp. bulbiferum3 1.31 0 100%
Colinus virginianus3 1.90 0 100%
Musca domestica3 1.90 0 92%

Seed sequence

129 residues. Every identity figure in this document is measured against this sequence.

KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL

Primary citations

One record per paper, not per entry.

YearCitation
2026 Unconventional chalcogen-containing azolylidene metal complexes as potential anticancer therapeutics. Chem Sci doi:10.1039/d5sc05555e
2026 A new macromolecular crystallography endstation at NanoTerasu for accelerating structural biology and drug discovery. Acta Crystallogr D Struct Biol doi:10.1107/S2059798325011234
2026 Binding of Aqueous-Stable, Lipophilic, Hemocompatible Anticancer V V O 2 Metallodrugs with Biological Molecules: X-ray Structures of the Adduct of the V V -hydrazonato Complex with Hen Egg White Lysozyme. Inorg.Chem. doi:10.1021/acs.inorgchem.5c05201
2026 Tuning Au Reactivity Beyond Canonical Targets: Ligand-Driven Au(I) Metalation of Lysine Residues in Hen Egg White Lysozyme. Inorg.Chem. doi:10.1021/acs.inorgchem.6c01884
2026 Unfolding of hen egg-white lysozyme - is there a unique starting point? J.Biomol.Struct.Dyn. doi:10.1080/07391102.2025.2475230
2026 A user-friendly goniometer-compatible fixed-target platform for macromolecular crystallography at synchrotrons. J.Appl.Crystallogr. doi:10.1107/S1600576725011513
2026 AI-Guided Droplet Microreactors Enable Rapid and Reproducible Protein Crystallization Small doi:10.1002/smll.202510977
2026 Drop-on-fixed-target reaction initiation approach for serial and time-resolved crystallography. Iucrj doi:10.1107/S2052252526003489
2026 Compact tape-driven sample delivery system for serial femtosecond crystallography. J.Appl.Crystallogr. doi:10.1107/S1600576726000063
2026 Guanosine hydrogel as a new injection matrix for protein serial X-ray crystallography Acta Crystallogr.,Sect.D doi:10.1107/S1600576725011276
2026 Covalently constrained 'Di-Gembodies' enable parallel structure solutions by cryo-EM. Nat.Chem.Biol. doi:10.1038/s41589-025-01972-7
2025 Exploring the potential of a bioassembler for protein crystallization in space. Npj Microgravity doi:10.1038/s41526-025-00477-w
2025 Structure and dynamics of the active site of hen egg-white lysozyme from atomic resolution neutron crystallography. Structure doi:10.1016/j.str.2024.10.030
2025 Unexpected in crystallo reactivity of the potential drug bis (maltolato) oxidovanadium (IV) with lysozyme Inorg Chem Front doi:10.1039/D4QI01528B
2025 Sensitive detection of structural dynamics using a statistical framework for comparative crystallography. Sci Adv doi:10.1126/sciadv.adj2921
2025 Speciation and structural transformation of a V V -malate complex in the absence and in the presence of a protein: from a dinuclear species to decavanadate. Inorg Chem Front doi:10.1039/d5qi01384d
2025 Finding the Key: Binding of Metal-Oxo Clusters to the Enzyme Active Site Enabled by "Click" (Bio)Conjugation. Angew.Chem.Int.Ed.Engl. doi:10.1002/anie.202518349
2025 Instrumentation and methods for efficient time-resolved X-ray crystallography of biomolecular systems with sub-10 ms time resolution. Iucrj doi:10.1107/S205225252500288X
2025 Automated gradient equilibration of macromolecular crystals to new solution conditions. Acta Crystallogr.,Sect.F doi:10.1107/S2053230X25008398
2025 Combining MicroED and native mass spectrometry for structural discovery of enzyme-small molecule complexes. Proc.Natl.Acad.Sci.USA doi:10.1073/pnas.2503780122
2025 Cytotoxicity and Binding to DNA, Lysozyme, Ribonuclease A, and Human Serum Albumin of the Diiodido Analog of Picoplatin. Inorg.Chem. doi:10.1021/acs.inorgchem.4c05424
2025 Protein crystallization and structure determination at room temperature in the CrystalChip. Febs Open Bio doi:10.1002/2211-5463.13932
2025 Laueprocess: a software package for processing Laue diffraction data. J.Appl.Crystallogr. doi:doi.org/10.1107/S1600576725005023
2025 Does crossing the pond affect crystal quality? Biorxiv doi:10.1101/2025.06.12.659325
2025 The structure of His15 acetamide-modified hen egg-white lysozyme: a nice surprise from an old friend. Acta Crystallogr.,Sect.F doi:10.1107/S2053230X2500010X
2025 Viscoelastic characterization of the lipid cubic phase provides insights into high-viscosity extrusion injection for XFEL experiments. Sci Rep doi:10.1038/s41598-025-25449-8
2025 Discrete Hybrid Vanadium-oxo Cluster as a Targeted Tool for Selective Protein Oxidative Modifications and Cleavage. Angew.Chem.Int.Ed.Engl. doi:10.1002/anie.202423078
2025 Real-time data processing for serial crystallography experiments. Iucrj doi:10.1107/S2052252524011837
2025 Formation of Mixed-Valence Cage-Like Polyoxidovanadates at 37°C Upon Reaction of V IV O(acetylacetonato) 2 With Lysozyme. Chemistry doi:10.1002/chem.202500488
2025 Fast and selective protein modification with iron-substituted polyoxometalates via a radical pathway Inorg Chem Front doi:10.1039/D5QI01454A
2025 Protein Recognition and Assembly by a Phosphocavitand. J.Am.Chem.Soc. doi:10.1021/jacs.5c08121
2025 Laueprocess: a software package for processing Laue diffraction data J.Appl.Crystallogr. doi:10.1107/S1600576725005023
2025 Advancing macromolecular structure determination with microsecond X-ray pulses at a 4th generation synchrotron. Commun Chem doi:10.1038/s42004-024-01404-y
2025 Dirhodium Tetraacetate Binding to Lysozyme at Body Temperature. Int J Mol Sci doi:10.3390/ijms26146582
2025 Spatially Aware Diffraction Mapping Enables Fully Autonomous MicroED. J.Am.Chem.Soc. doi:10.1021/jacs.5c10751
2024 Exploring the coordination chemistry of ruthenium complexes with lysozymes: structural and in-solution studies. Front Chem doi:10.3389/fchem.2024.1371637
2024 Time-series analysis of rhenium(I) organometallic covalent binding to a model protein for drug development. Iucrj doi:10.1107/S2052252524002598
2024 Non-Covalent and Covalent Binding of New Mixed-Valence Cage-like Polyoxidovanadate Clusters to Lysozyme. Angew.Chem.Int.Ed.Engl. doi:10.1002/anie.202406669
2024 Interaction of V V O 2 -hydrazonates with lysozyme. J.Inorg.Biochem. doi:10.1016/j.jinorgbio.2024.112787
2024 Protein-Protein Stabilization in V IV O/8-Hydroxyquinoline-Lysozyme Adducts. Chemistry doi:10.1002/chem.202401712