MolNFT v1 · #136717 · protein

Crystal structure of streptococcus suis suib

5V1Q · Radical SAM: “Crystal structure of streptococcus suis suib”. X-ray diffraction, 1 ligand (SF4), 7 pockets (best druggability 0.82). MolNFT v1 #136717 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5V1Q
Type: protein
Length: 868 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Radical SAM
UniProt: A0A0Z8EWX1
Ligands: SF4
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Radical SAM	protein	428	39% helix, 14% strand	A0A0Z8EWX1
B	Radical SAM	protein	440	40% helix, 15% strand	A0A0Z8EWX1

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1170	0.82	0.83	101	SF4
2	1111	0.82	0.83	89	SF4
3	756	0.67	0.74	66	empty
4	54	0.65	0.95	19	SF4
5	80	0.64	0.91	23	SF4

Interfaces

1 interface between chains.

A–B · 103 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5V1Q · Crystal structure of Streptococcus suis SuiB · 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 A0A0Z8EWX1
Elsewhere: RCSB PDB 5V1Q · PDBe 5V1Q · UniProt A0A0Z8EWX1

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