MolNFT v1 · #168000 · protein

Structures of capsid and capsid-associated tegument complex inside the epstein-barr virus

6W2D · Major capsid protein: “Structures of capsid and capsid-associated tegument complex inside the epstein-barr virus”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #168000 on GenesisL1: 3D structure, binding sites…

PDB: 6W2D
Type: protein
Length: 9,430 residues
Chains: 21
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major capsid protein; Capsid vertex component 1; Capsid vertex component 2; Large…
EC: 3.4.19.12, 3.4.22.-
UniProt: P03226, P03222, P03233, P03186, P14348, P03187, P25214
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 13 distinct chains · 36% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
J	Major capsid protein	protein	1352	36% helix, 16% strand	P03226
K	Major capsid protein	protein	1381	36% helix, 16% strand	P03226
N	Major capsid protein	protein	1362	36% helix, 17% strand	P03226
O	Major capsid protein	protein	1332	36% helix, 19% strand	P03226
P	Major capsid protein	protein	1283	36% helix, 16% strand	P03226
v	Capsid vertex component 1	protein	292	27% helix, 20% strand	P03222
w, x	Capsid vertex component 2	protein	68	84% helix, 0% strand	P03233
y, z	Large tegument protein deneddylase (EC 3.4.19.12, 3.4.22.-)	protein	37	89% helix, 0% strand	P03186
Z, a, d, e	Small capsomere-interacting protein	protein	77	57% helix, 0% strand	P14348
u	Small capsomere-interacting protein	protein	63	52% helix, 0% strand	P14348
f	Triplex capsid protein 1	protein	315	25% helix, 28% strand	P03187
h	Triplex capsid protein 1	protein	336	24% helix, 27% strand	P03187
k, m, p, r	Triplex capsid protein 2	protein	299	35% helix, 20% strand	P25214

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	636	0.87	0.91	88	empty
2	1063	0.86	0.86	106	empty
3	1046	0.85	0.86	103	empty
4	684	0.85	0.89	95	empty
5	716	0.85	0.89	86	empty

Interfaces

47 interfaces between chains.

N–O · 6161 Å² buried · 57 hydrogen bonds · protein-protein
J–K · 6125 Å² buried · 62 hydrogen bonds · protein-protein
J–O · 5551 Å² buried · 53 hydrogen bonds · protein-protein
k–p · 3487 Å² buried · 16 hydrogen bonds · protein-protein
m–r · 3418 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6W2D · Structures of Capsid and Capsid-Associated Tegument Complex inside the Epstein-Barr Virus · the same entry in another collection · chain J against J, 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 P03226
Every structure of UniProt P03222
Every structure of UniProt P03233
Every structure of UniProt P03186
Every structure of UniProt P14348
Every structure of UniProt P03187
Every structure of UniProt P25214
Elsewhere: RCSB PDB 6W2D · PDBe 6W2D · UniProt P03226 · UniProt P03222 · UniProt P03233 · UniProt P03186 · UniProt P14348 · UniProt P03187 · UniProt P25214

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