Research workbench

SARS-COV2 rbd bound to FAB06

Analyse SARS-COV2 rbd bound to FAB06 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7WPH
Type: protein
Length: 1,242 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; Fab light chain; Fab heavy chain
UniProt: P0DTC2
Ligands: NAG
Pockets: 8 · best druggability 0.64

Structure

x-ray diffraction · 6 distinct chains · 10% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike protein S1	protein	196	19% helix, 29% strand	P0DTC2
B	Spike protein S1	protein	195	15% helix, 28% strand	P0DTC2
D	Fab light chain	protein	212	6% helix, 49% strand	—
E	Fab heavy chain	protein	210	9% helix, 51% strand	—
H	Fab heavy chain	protein	218	6% helix, 51% strand	—
L	Fab light chain	protein	211	6% helix, 50% strand	—

Ligands and binding sites

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

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	689	0.64	0.74	77	empty
2	653	0.63	0.74	53	empty
3	208	0.48	0.75	41	empty
4	77	0.35	0.76	20	empty
5	90	0.32	0.73	18	empty

Interfaces

7 interfaces between chains.

D–E · 1738 Å² buried · 15 hydrogen bonds · protein-protein
H–L · 1676 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 454 Å² buried · 14 hydrogen bonds · protein-protein
B–H · 440 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 379 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7WPH · SARS-CoV2 RBD bound to Fab06 · 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
Elsewhere: RCSB PDB 7WPH · PDBe 7WPH · UniProt P0DTC2

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