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

Analyse KAPOSI'S sarcoma-associated herpesvirus (kshv), C1 penton vertex register… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PPD
Type: protein
Length: 8,728 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Small capsomere-interacting protein; Major capsid protein; Triplex capsid protein 1…
UniProt: Q76RF4, D0UZN7, Q76RF6, C7E5A9
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 12 distinct chains · 31% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0, 2, 3, 1	Small capsomere-interacting protein	protein	78	53% helix, 0% strand	Q76RF4
W	Major capsid protein	protein	1354	32% helix, 17% strand	D0UZN7
S	Major capsid protein	protein	1281	30% helix, 17% strand	D0UZN7
T	Major capsid protein	protein	1360	33% helix, 16% strand	D0UZN7
4	Major capsid protein	protein	1222	32% helix, 14% strand	D0UZN7
A	Small capsomere-interacting protein	protein	44	68% helix, 0% strand	Q76RF4
5	Triplex capsid protein 1	protein	314	23% helix, 28% strand	Q76RF6
6, c	Triplex capsid protein 2	protein	294	30% helix, 21% strand	C7E5A9
7	Triplex capsid protein 2	protein	291	29% helix, 18% strand	C7E5A9
b	Triplex capsid protein 1	protein	321	20% helix, 28% strand	Q76RF6
d	Triplex capsid protein 2	protein	300	36% helix, 22% strand	C7E5A9
X	Major capsid protein	protein	1341	32% helix, 18% 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	1105	0.88	0.89	142	empty
2	587	0.88	0.93	90	empty
3	994	0.88	0.89	126	empty
4	1155	0.87	0.89	128	empty
5	1015	0.86	0.88	107	empty

Interfaces

41 interfaces between chains.

W–X · 6564 Å² buried · 52 hydrogen bonds · protein-protein
S–T · 6486 Å² buried · 56 hydrogen bonds · protein-protein
6–7 · 3509 Å² buried · 14 hydrogen bonds · protein-protein
c–d · 3481 Å² buried · 16 hydrogen bonds · protein-protein
W–T · 2456 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6PPD · Kaposi's sarcoma-associated herpesvirus (KSHV), C1 penton vertex register, CATC-absent… · the same entry in another collection · chain 0 against 0, 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 Q76RF4
Every structure of UniProt D0UZN7
Every structure of UniProt Q76RF6
Every structure of UniProt C7E5A9
Elsewhere: RCSB PDB 6PPD · PDBe 6PPD · UniProt Q76RF4 · UniProt D0UZN7 · UniProt Q76RF6 · UniProt C7E5A9

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