Research workbench

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: 2YGC
Type: protein
Length: 1,626 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 0.83

Structure

x-ray diffraction · 1 distinct chain · 17% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Rifampicin resistance protein	protein	542	17% helix, 39% strand	P68440

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1097	0.83	0.84	112	empty
2	693	0.82	0.86	80	empty
3	701	0.81	0.85	83	empty
4	366	0.70	0.83	42	empty
5	517	0.70	0.80	51	empty

Interfaces

3 interfaces between chains.

A–B · 2895 Å² buried · 38 hydrogen bonds · protein-protein
B–C · 2827 Å² buried · 32 hydrogen bonds · protein-protein
A–C · 2794 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

2YGC · Structure of vaccinia virus D13 scaffolding protein · the same entry in another collection · chain C against C, 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 2YGC · PDBe 2YGC · UniProt P68440

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.