MolNFT v1 · #149829 · protein

Crystal structure of the oligomerization domain of VP35 from reston virus, mercury derivative

6GBR · Polymerase cofactor VP35: “Crystal structure of the oligomerization domain of VP35 from reston virus, mercury derivative”. X-ray diffraction, 1 ligand (MBO), 2 pockets (best druggability 0.57). MolNFT v1 #149829 on GenesisL1: 3D…

PDB: 6GBR
Type: protein
Length: 270 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polymerase cofactor VP35
UniProt: Q8JPY0
Ligands: MBO
Pockets: 2 · best druggability 0.57

Structure

x-ray diffraction · 4 distinct chains · 93% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polymerase cofactor VP35	protein	67	96% helix, 0% strand	Q8JPY0
B	Polymerase cofactor VP35	protein	66	92% helix, 0% strand	Q8JPY0
C	Polymerase cofactor VP35	protein	70	93% helix, 0% strand	Q8JPY0
D	Polymerase cofactor VP35	protein	67	93% helix, 0% strand	Q8JPY0

Ligands and binding sites

MBO · Mercuribenzoic acid · ligand · 2 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	100	0.57	0.85	13	empty
2	65	0.41	0.80	11	empty

Interfaces

6 interfaces between chains.

A–D · 1647 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 1615 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1253 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1203 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 573 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6GBR · Crystal Structure of the oligomerization domain of VP35 from Reston virus, mercury… · 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 Q8JPY0
Elsewhere: RCSB PDB 6GBR · PDBe 6GBR · UniProt Q8JPY0

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