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Crystal structure of SARS-cov-2 S delta variant receptor-binding domain (rbd) in complex COV11 Fab crystal form 1

Analyse Crystal structure of SARS-cov-2 S delta variant receptor-binding domain (rbd)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7URQ
Type: protein
Length: 625 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; COV11 Fab heavy chain; COV11 Fab light chain
UniProt: P0DTC2
Ligands: NAG
Pockets: 7 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike protein S1	protein	196	17% helix, 30% strand	P0DTC2
H	COV11 Fab heavy chain	protein	214	9% helix, 53% strand	—
L	COV11 Fab light chain	protein	215	7% helix, 53% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
CIT · Citric acid · additive · chains A, H

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	192	0.65	0.85	24	empty
2	492	0.59	0.74	59	empty
3	67	0.57	0.89	27	empty
4	125	0.40	0.75	25	empty
5	117	0.39	0.74	24	empty

Interfaces

3 interfaces between chains.

H–L · 1727 Å² buried · 12 hydrogen bonds · protein-protein
A–H · 898 Å² buried · 17 hydrogen bonds · protein-protein
A–L · 370 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7URQ · Crystal Structure of SARS-CoV-2 S delta variant receptor-binding domain (RBD) in complex… · 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 7URQ · PDBe 7URQ · UniProt P0DTC2

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