MolNFT v1 · #156510 · protein

Structure of HSV2 B-capsid portal vertex

6M6I · Major capsid protein: “Structure of HSV2 B-capsid portal vertex”. Electron microscopy, 20 pockets (best druggability 0.90). MolNFT v1 #156510 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6M6I
Type: protein
Length: 9,791 residues
Chains: 17
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major capsid protein; Coiled coils chain 1; Coiled coils chain 2; Triplex capsid protein…
UniProt: P89442, G9I239, G9I260, G9I257
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 11 distinct chains · 29% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major capsid protein	protein	1350	29% helix, 13% strand	P89442
B, C	Major capsid protein	protein	1362	28% helix, 14% strand	P89442
D	Major capsid protein	protein	1360	29% helix, 15% strand	P89442
E	Major capsid protein	protein	1345	27% helix, 14% strand	P89442
F	Major capsid protein	protein	1351	27% helix, 12% strand	P89442
G	Coiled coils chain 1	protein	81	78% helix, 0% strand	—
H	Coiled coils chain 2	protein	83	55% helix, 0% strand	—
I	Triplex capsid protein 2	protein	299	33% helix, 18% strand	G9I239
J	Triplex capsid protein 2	protein	307	32% helix, 19% strand	G9I239
K	Triplex capsid protein 1	protein	285	19% helix, 17% strand	G9I260
L, M, N, O, P, Q	Small capsomere-interacting protein	protein	101	35% helix, 0% strand	G9I257

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	1112	0.90	0.92	169	empty
2	628	0.87	0.92	100	empty
3	960	0.87	0.88	124	empty
4	614	0.86	0.90	97	empty
5	1181	0.85	0.86	121	empty

Interfaces

37 interfaces between chains.

B–C · 6170 Å² buried · 68 hydrogen bonds · protein-protein
C–D · 6048 Å² buried · 69 hydrogen bonds · protein-protein
A–B · 5889 Å² buried · 65 hydrogen bonds · protein-protein
D–E · 5832 Å² buried · 67 hydrogen bonds · protein-protein
E–F · 5788 Å² buried · 58 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

6M6I · Structure of HSV2 B-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 G9I239
Every structure of UniProt G9I260
Every structure of UniProt G9I257
Elsewhere: RCSB PDB 6M6I · PDBe 6M6I · UniProt P89442 · UniProt G9I239 · UniProt G9I260 · UniProt G9I257

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