Research workbench

Epstein-barr virus, C1 portal-proximal penton vertex, catc binding

Analyse Epstein-barr virus, C1 portal-proximal penton vertex, catc binding in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7BR7
Type: protein
Length: 9,263 residues
Chains: 21
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid vertex component 2; Capsid vertex component 1; Large tegument protein deneddylase…
EC: 3.4.19.12, 3.4.22.-
UniProt: P03233, P03222, P03186, P14348, P03226, P03187, P25214
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 18 distinct chains · 34% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
K	Capsid vertex component 2	protein	68	69% helix, 3% strand	P03233
G	Capsid vertex component 2	protein	84	56% helix, 4% strand	P03233
C	Capsid vertex component 1	protein	346	29% helix, 20% strand	P03222
B	Large tegument protein deneddylase (EC 3.4.19.12, 3.4.22.-)	protein	35	80% helix, 0% strand	P03186
O	Large tegument protein deneddylase (EC 3.4.19.12, 3.4.22.-)	protein	29	90% helix, 0% strand	P03186
m	Small capsomere-interacting protein	protein	71	44% helix, 0% strand	P14348
Y, Z, 2, y	Small capsomere-interacting protein	protein	74	47% helix, 0% strand	P14348
S	Major capsid protein	protein	1327	34% helix, 15% strand	P03226
T	Major capsid protein	protein	1305	32% helix, 18% strand	P03226
W	Major capsid protein	protein	1331	35% helix, 15% strand	P03226
x	Major capsid protein	protein	1325	33% helix, 15% strand	P03226
e	Triplex capsid protein 1	protein	319	25% helix, 29% strand	P03187
f	Triplex capsid protein 2	protein	290	35% helix, 22% strand	P25214
g	Triplex capsid protein 2	protein	290	31% helix, 17% strand	P25214
l	Major capsid protein	protein	1250	35% helix, 16% strand	P03226
5	Triplex capsid protein 1	protein	313	30% helix, 27% strand	P03187
6	Triplex capsid protein 2	protein	297	34% helix, 19% strand	P25214
7	Triplex capsid protein 2	protein	287	39% helix, 18% 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	1011	0.87	0.88	110	empty
2	826	0.87	0.89	101	empty
3	799	0.86	0.89	136	empty
4	979	0.86	0.88	123	empty
5	884	0.86	0.88	77	empty

Interfaces

60 interfaces between chains.

W–x · 6133 Å² buried · 69 hydrogen bonds · protein-protein
S–T · 5978 Å² buried · 65 hydrogen bonds · protein-protein
f–g · 3499 Å² buried · 29 hydrogen bonds · protein-protein
6–7 · 3299 Å² buried · 25 hydrogen bonds · protein-protein
S–x · 2412 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

7BR7 · Epstein-Barr virus, C1 portal-proximal penton vertex, CATC binding · the same entry in another collection · chain K against K, 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 P03233
Every structure of UniProt P03222
Every structure of UniProt P03186
Every structure of UniProt P14348
Every structure of UniProt P03226
Every structure of UniProt P03187
Every structure of UniProt P25214
Elsewhere: RCSB PDB 7BR7 · PDBe 7BR7 · UniProt P03233 · UniProt P03222 · UniProt P03186 · UniProt P14348 · UniProt P03226 · UniProt P03187 · UniProt P25214

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