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Crystal structure of reovirus T3D attachment protein SIGMA1 head domain D345N mutant

Analyse Crystal structure of reovirus T3D attachment protein SIGMA1 head domain D345N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2OJ6
Type: protein
Length: 969 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Viral attachment protein sigma 1
UniProt: Q86337
Ligands: MG
Pockets: 6 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F	Viral attachment protein sigma 1	protein	162	5% helix, 59% strand	Q86337
C	Viral attachment protein sigma 1	protein	162	5% helix, 60% strand	Q86337
D	Viral attachment protein sigma 1	protein	160	5% helix, 59% strand	Q86337
E	Viral attachment protein sigma 1	protein	161	5% helix, 59% strand	Q86337

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B, E

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	486	0.87	0.95	42	empty
2	454	0.87	0.94	40	empty
3	862	0.72	0.77	72	MG
4	57	0.42	0.82	23	empty
5	132	0.40	0.74	17	empty

Interfaces

8 interfaces between chains.

B–C · 1223 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 1212 Å² buried · 23 hydrogen bonds · protein-protein
D–F · 1206 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1198 Å² buried · 19 hydrogen bonds · protein-protein
D–E · 1193 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

2OJ6 · Crystal Structure of Reovirus T3D Attachment Protein Sigma1 head domain D345N mutant · 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 Q86337
Elsewhere: RCSB PDB 2OJ6 · PDBe 2OJ6 · UniProt Q86337

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