MolNFT v1 · #156509 · protein

Structure of HSV2 C-capsid portal vertex

6M6H · Major capsid protein: “Structure of HSV2 C-capsid portal vertex”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #156509 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6M6H
Type: protein
Length: 10,426 residues
Chains: 20
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major capsid protein; Capsid vertex component 1; Capsid vertex component 2; Small…
EC: 3.4.19.12, 3.4.22.-
UniProt: P89442, P89440, P89448, G9I257, P89459, G9I239, G9I260
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 12 distinct chains · 29% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major capsid protein	protein	1319	28% helix, 10% strand	P89442
B, C, D	Major capsid protein	protein	1362	29% helix, 12% strand	P89442
E	Major capsid protein	protein	1351	27% helix, 15% strand	P89442
F	Major capsid protein	protein	1351	28% helix, 12% strand	P89442
G	Capsid vertex component 1	protein	554	33% helix, 17% strand	P89440
H	Capsid vertex component 2	protein	94	33% helix, 4% strand	P89448
I	Capsid vertex component 2	protein	80	41% helix, 1% strand	P89448
J, K, L, M, N, O	Small capsomere-interacting protein	protein	101	34% helix, 0% strand	G9I257
P, Q	Large tegument protein deneddylase (EC 3.4.19.12, 3.4.22.-)	protein	47	60% helix, 0% strand	P89459
R	Triplex capsid protein 2	protein	299	33% helix, 16% strand	G9I239
S	Triplex capsid protein 2	protein	307	25% helix, 18% strand	G9I239
T	Triplex capsid protein 1	protein	285	18% helix, 14% strand	G9I260

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	1157	0.89	0.91	180	empty
2	703	0.88	0.92	106	empty
3	1044	0.87	0.88	141	empty
4	665	0.86	0.91	94	empty
5	797	0.86	0.88	89	empty

Interfaces

45 interfaces between chains.

C–D · 6057 Å² buried · 68 hydrogen bonds · protein-protein
A–B · 5981 Å² buried · 64 hydrogen bonds · protein-protein
D–E · 5977 Å² buried · 70 hydrogen bonds · protein-protein
B–C · 5876 Å² buried · 61 hydrogen bonds · protein-protein
E–F · 5848 Å² buried · 65 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

6M6H · Structure of HSV2 C-capsid portal vertex · the same entry in another collection · chain A against A, 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 P89442
Every structure of UniProt P89440
Every structure of UniProt P89448
Every structure of UniProt G9I257
Every structure of UniProt P89459
Every structure of UniProt G9I239
Every structure of UniProt G9I260
Elsewhere: RCSB PDB 6M6H · PDBe 6M6H · UniProt P89442 · UniProt P89440 · UniProt P89448 · UniProt G9I257 · UniProt P89459 · UniProt G9I239 · UniProt G9I260

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