MolNFT v1 · #170865 · protein

Crystal structure of the SARS-cov-2 receptor binding domain in complex with CR3022 Fab

6YLA · Spike glycoprotein: “Crystal structure of the SARS-cov-2 receptor binding domain in complex with CR3022 Fab”. X-ray diffraction, 1 ligand (NAG), 13 pockets (best druggability 0.80). MolNFT v1 #170865 on GenesisL1: 3D structure…

PDB: 6YLA
Type: protein
Length: 1,273 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein; Heavy chain; Light chain
UniProt: P0DTC2
Ligands: NAG
Pockets: 13 · best druggability 0.80

Structure

x-ray diffraction · 5 distinct chains · 9% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Spike glycoprotein	protein	203	11% helix, 29% strand	P0DTC2
H	Heavy chain	protein	216	9% helix, 53% strand	—
L, C	Light chain	protein	219	5% helix, 53% strand	—
A	Spike glycoprotein	protein	199	14% helix, 29% strand	P0DTC2
B	Heavy chain	protein	217	8% helix, 53% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains E, A
DMS · Dimethyl sulfoxide · additive · 14 copies · chains E, H, B, L, A, C
MLI · Malonate ion · additive · 12 copies · chains E, H, L, B, A, C
1PE · Pentaethylene glycol · additive · 2 copies · chains H, L, B, C
PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1152	0.80	0.81	81	MLI
2	447	0.72	0.82	66	MLI
3	308	0.71	0.85	42	empty
4	549	0.67	0.78	70	1PE
5	239	0.54	0.77	37	empty

Interfaces

12 interfaces between chains.

B–C · 1821 Å² buried · 17 hydrogen bonds · protein-protein
H–L · 1808 Å² buried · 16 hydrogen bonds · protein-protein
E–H · 668 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 650 Å² buried · 10 hydrogen bonds · protein-protein
H–B · 574 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

6YLA · Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab · the same entry in another collection · chain E against E, 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 6YLA · PDBe 6YLA · UniProt P0DTC2

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