Research workbench

S protein of SARS-cov-2 in complex bound with FABP5A-2G7

Analyse S protein of SARS-cov-2 in complex bound with FABP5A-2G7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7D03
Type: protein
Length: 3,412 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein; Immunoglobulin heavy variable 4-61,CHAIN H of FABP5A-2G7, epididymis…
UniProt: P0DTC2, A0A0C4DH41, V9HW68, A0A5C2G2G8, Q6IPQ0
Ligands: NAG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 4 distinct chains · 17% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	1006	21% helix, 32% strand	P0DTC2
B, C	Spike glycoprotein	protein	981	19% helix, 31% strand	P0DTC2
H	Immunoglobulin heavy variable 4-61,CHAIN H of FABP5A-2G7, epididymis luminal protein 214	protein	230	4% helix, 45% strand	A0A0C4DH41, V9HW68
L	Igl C2312_LIGHT_IGLV2-14_IGLJ2,IGL@ protein	protein	214	5% helix, 41% strand	A0A5C2G2G8, Q6IPQ0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 69 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	928	0.86	0.88	130	empty
2	651	0.82	0.87	69	empty
3	982	0.81	0.82	90	empty
4	605	0.80	0.86	71	empty
5	1071	0.80	0.81	101	empty

Interfaces

6 interfaces between chains.

B–C · 4908 Å² buried · 35 hydrogen bonds · protein-protein
A–C · 4619 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 4239 Å² buried · 28 hydrogen bonds · protein-protein
H–L · 1879 Å² buried · 8 hydrogen bonds · protein-protein
A–H · 739 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 glycan, 39 disulfide (N-glycosylation, disulfide).

Compared structures

7D03 · S protein of SARS-CoV-2 in complex bound with FabP5A-2G7 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P0DTC2
Every structure of UniProt A0A0C4DH41
Every structure of UniProt V9HW68
Every structure of UniProt A0A5C2G2G8
Every structure of UniProt Q6IPQ0
Elsewhere: RCSB PDB 7D03 · PDBe 7D03 · UniProt P0DTC2 · UniProt A0A0C4DH41 · UniProt V9HW68 · UniProt A0A5C2G2G8 · UniProt Q6IPQ0

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