Spike glycoprotein

Severe acute respiratory syndrome coronavirus 2 · seed P0DTC2 · 1273 aa · family defined as ≥30% identity to that seed · compiled 07 October 2026

Open in CODSWALLOP UniProt P0DTC2 RCSB by accession PDBe-KB AlphaFold DB InterPro CATH 2.60.120.960 CATH 2.60.40.10 SCOP 8037105 SCOP 8092469 SCOP 8092467 SCOP 8092661 SCOP 8092663 SCOP 8092471 SCOP 8092473 RCSB 7EAN 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.

The reference structure

7EAN, 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.

Which residues anyone has ever seen

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.

Constructs, most-used first

821 distinct constructs across 1,991 entries. 1,968 polymer entities differ from the UniProt canonical sequence in some way, 601 carry a recognised expression tag and 5 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.

Showing the 25 most-used of 821.

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".

What it assembles into

458 entries have the depositor's assembly corroborated by PISA, 1,526 carry the depositor's word alone and 7 were assigned by PISA where the depositor gave none. The middle figure is not a disagreement: PISA may have returned nothing or never run. 4 entries carry more than one assembly with different chain counts, so they have no single answer to quote: 3D0H, 3D0I, 8ELP, 9JTD.

Domain architecture

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.

What binds it

NAG1401 entries EIC26 entries BLA17 entries MAN10 entries NDG3 entries PG03 entries PRO3 entries BLR3 entries LEU2 entries FOL2 entries FUC2 entries VCG2 entries

How it crystallises

Parsed from the free text 545 depositors typed into _exptl_crystal_grow.pdbx_details, out of 545 entries that recorded anything at all. Median pH 7.0 (range 3.3 to 10.5).

Precipitants

Buffers

Which entries to trust

1,986 entries carry a wwPDB validation report: 1,465 clean, 399 worth a check and 122 with something to explain. Median clashscore 6.02, median RSRZ outliers 3.72%, median R-free minus R-work 0.041. 1,984 have released structure factors.

Across species

Seed sequence

1273 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.

Primary citations

One record per paper, not per entry.