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Structure of vaccinia virus D13 scaffolding protein

Analyse Structure of vaccinia virus D13 scaffolding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YGB
Type: protein
Length: 1,600 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rifampicin resistance protein
UniProt: P68440
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Rifampicin resistance protein	protein	533	15% helix, 41% strand	P68440
B	Rifampicin resistance protein	protein	534	15% helix, 41% strand	P68440

Pockets

20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1052	0.84	0.85	112	empty
2	948	0.83	0.84	99	empty
3	1045	0.83	0.84	99	empty
4	407	0.62	0.78	46	empty
5	247	0.52	0.75	37	empty

Interfaces

3 interfaces between chains.

A–B · 2296 Å² buried · 32 hydrogen bonds · protein-protein
B–C · 2280 Å² buried · 30 hydrogen bonds · protein-protein
A–C · 2269 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

2YGB · Structure of vaccinia virus D13 scaffolding protein · 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 P68440
Elsewhere: RCSB PDB 2YGB · PDBe 2YGB · UniProt P68440

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