MolNFT v1 · #160605 · protein

KAPOSI'S sarcoma-associated herpesvirus (kshv), C5 portal vertex structure

6PPB · Capsid vertex component 1: “KAPOSI'S sarcoma-associated herpesvirus (kshv), C5 portal vertex structure”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #160605 on GenesisL1: 3D structure, binding sites and…

PDB: 6PPB
Type: protein
Length: 7,953 residues
Chains: 19
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid vertex component 1; Capsid vertex component 2; Large tegument protein deneddylase…
EC: 3.4.19.12, 3.4.22.-
UniProt: Q76RH8, Q76RI7, Q2HR64, Q2HRA7, Q76RF6, Q98832, Q76RF4
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 14 distinct chains · 32% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
k	Capsid vertex component 1	protein	344	30% helix, 23% strand	Q76RH8
l	Capsid vertex component 2	protein	83	77% helix, 1% strand	Q76RI7
m	Capsid vertex component 2	protein	80	71% helix, 1% strand	Q76RI7
n, o	Large tegument protein deneddylase (EC 3.4.19.12, 3.4.22.-)	protein	40	88% helix, 0% strand	Q2HR64
S	Major capsid protein	protein	1281	28% helix, 16% strand	Q2HRA7
T	Major capsid protein	protein	1360	33% helix, 16% strand	Q2HRA7
W	Major capsid protein	protein	1354	33% helix, 15% strand	Q2HRA7
X	Major capsid protein	protein	1288	31% helix, 17% strand	Q2HRA7
b	Triplex capsid protein 1	protein	321	23% helix, 27% strand	Q76RF6
c, 6	Triplex capsid protein 2	protein	294	32% helix, 19% strand	Q98832
d	Triplex capsid protein 2	protein	300	37% helix, 22% strand	Q98832
5	Triplex capsid protein 1	protein	268	21% helix, 26% strand	Q76RF6
7	Triplex capsid protein 2	protein	294	34% helix, 18% strand	Q98832
0, 1, 2, 3	Small capsomere-interacting protein	protein	78	58% helix, 0% strand	Q76RF4

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	875	0.89	0.92	125	empty
2	1115	0.89	0.90	145	empty
3	826	0.88	0.91	111	empty
4	1153	0.88	0.89	155	empty
5	1052	0.87	0.88	118	empty

Interfaces

47 interfaces between chains.

S–T · 6491 Å² buried · 53 hydrogen bonds · protein-protein
W–X · 6446 Å² buried · 41 hydrogen bonds · protein-protein
S–X · 5200 Å² buried · 50 hydrogen bonds · protein-protein
6–7 · 3598 Å² buried · 18 hydrogen bonds · protein-protein
c–d · 3583 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

6PPB · Kaposi's sarcoma-associated herpesvirus (KSHV), C5 portal vertex structure · 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 Q76RH8
Every structure of UniProt Q76RI7
Every structure of UniProt Q2HR64
Every structure of UniProt Q2HRA7
Every structure of UniProt Q76RF6
Every structure of UniProt Q98832
Every structure of UniProt Q76RF4
Elsewhere: RCSB PDB 6PPB · PDBe 6PPB · UniProt Q76RH8 · UniProt Q76RI7 · UniProt Q2HR64 · UniProt Q2HRA7 · UniProt Q76RF6 · UniProt Q98832 · UniProt Q76RF4

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