MolNFT v1 · #106151 · protein

Crystal structure of the natually occurring empty particle of a clinical C4 strain EV71

4RQP · Capsid protein VP1: “Crystal structure of the natually occurring empty particle of a clinical C4 strain EV71”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #106151 on GenesisL1: 3D structure, binding sites and…

PDB: 4RQP
Type: protein
Length: 3,430 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein VP1; Capsid protein VP3; Capsid protein VP0
UniProt: F6KTB0
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, Q, I, M, A	Capsid protein VP1	protein	223	8% helix, 34% strand	F6KTB0
F, R, J, N, B	Capsid protein VP3	protein	225	11% helix, 33% strand	F6KTB0
G, S, K, O, C	Capsid protein VP0	protein	238	10% helix, 34% strand	F6KTB0

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	961	0.80	0.82	98	empty
2	1087	0.80	0.81	101	empty
3	955	0.79	0.81	91	empty
4	904	0.79	0.81	80	empty
5	1105	0.78	0.80	96	empty

Interfaces

50 interfaces between chains.

Q–R · 3037 Å² buried · 38 hydrogen bonds · protein-protein
E–F · 3005 Å² buried · 42 hydrogen bonds · protein-protein
M–N · 2993 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 2983 Å² buried · 34 hydrogen bonds · protein-protein
I–J · 2982 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

4RQP · Crystal structure of the natually occurring empty particle of a clinical C4 strain EV71 · 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 F6KTB0
Elsewhere: RCSB PDB 4RQP · PDBe 4RQP · UniProt F6KTB0

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