MolNFT v1 · #160611 · protein

KAPOSI'S sarcoma-associated herpesvirus (kshv), C1 penton vertex register, catc-binding structure

6PPH · Capsid vertex component 1: “KAPOSI'S sarcoma-associated herpesvirus (kshv), C1 penton vertex register, catc-binding structure”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #160611 on GenesisL1: 3D structure…

PDB: 6PPH
Type: protein
Length: 9,326 residues
Chains: 21
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, Q76RF6, C7E5A9, D0UZN7, Q76RF4
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 17 distinct chains · 32% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
k	Capsid vertex component 1	protein	344	30% helix, 24% strand	Q76RH8
l	Capsid vertex component 2	protein	83	77% helix, 2% strand	Q76RI7
m	Capsid vertex component 2	protein	80	70% helix, 1% strand	Q76RI7
n, o	Large tegument protein deneddylase (EC 3.4.19.12, 3.4.22.-)	protein	40	90% helix, 0% strand	Q2HR64
5	Triplex capsid protein 1	protein	314	23% helix, 27% strand	Q76RF6
6	Triplex capsid protein 2	protein	302	34% helix, 21% strand	C7E5A9
7	Triplex capsid protein 2	protein	294	33% helix, 23% strand	C7E5A9
b	Triplex capsid protein 1	protein	321	23% helix, 27% strand	Q76RF6
c	Triplex capsid protein 2	protein	294	29% helix, 20% strand	C7E5A9
d	Triplex capsid protein 2	protein	300	35% helix, 22% strand	C7E5A9
4	Major capsid protein	protein	1222	31% helix, 14% strand	D0UZN7
A	Small capsomere-interacting protein	protein	44	66% helix, 0% strand	Q76RF4
2, 3, 1, 0	Small capsomere-interacting protein	protein	78	59% helix, 0% strand	Q76RF4
S	Major capsid protein	protein	1281	28% helix, 18% strand	D0UZN7
T	Major capsid protein	protein	1360	31% helix, 16% strand	D0UZN7
X	Major capsid protein	protein	1341	31% helix, 18% strand	D0UZN7
W	Major capsid protein	protein	1354	31% helix, 16% strand	D0UZN7

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	1130	0.89	0.91	144	empty
2	719	0.87	0.91	104	empty
3	940	0.87	0.89	109	empty
4	1109	0.87	0.88	128	empty
5	532	0.87	0.93	88	empty

Interfaces

60 interfaces between chains.

X–W · 6480 Å² buried · 54 hydrogen bonds · protein-protein
S–T · 6446 Å² buried · 58 hydrogen bonds · protein-protein
6–7 · 3628 Å² buried · 17 hydrogen bonds · protein-protein
c–d · 3477 Å² buried · 17 hydrogen bonds · protein-protein
T–W · 2505 Å² buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

6PPH · Kaposi's sarcoma-associated herpesvirus (KSHV), C1 penton vertex register, 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 Q76RH8
Every structure of UniProt Q76RI7
Every structure of UniProt Q2HR64
Every structure of UniProt Q76RF6
Every structure of UniProt C7E5A9
Every structure of UniProt D0UZN7
Every structure of UniProt Q76RF4
Elsewhere: RCSB PDB 6PPH · PDBe 6PPH · UniProt Q76RH8 · UniProt Q76RI7 · UniProt Q2HR64 · UniProt Q76RF6 · UniProt C7E5A9 · UniProt D0UZN7 · UniProt Q76RF4

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