Research workbench

SARS-cov-2 delta rbd and NB22

Analyse SARS-cov-2 delta rbd and NB22 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7X7D
Type: protein
Length: 972 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; NB22
UniProt: P0DTC2
Pockets: 11 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, A, E	Spike protein S1	protein	194	15% helix, 29% strand	P0DTC2
C, B, F	NB22	protein	130	9% helix, 47% strand	—

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	78	0.74	0.96	18	empty
2	592	0.73	0.81	55	empty
3	637	0.73	0.80	58	empty
4	172	0.72	0.89	28	empty
5	1096	0.72	0.76	99	empty

Interfaces

12 interfaces between chains.

E–F · 929 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 904 Å² buried · 15 hydrogen bonds · protein-protein
D–C · 899 Å² buried · 16 hydrogen bonds · protein-protein
C–F · 388 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 384 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

7X7D · SARS-CoV-2 Delta RBD and Nb22 · the same entry in another collection · chain D against D, 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 7X7D · PDBe 7X7D · UniProt P0DTC2

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