MolNFT v1 · #107934 · protein

Crystal structure of staph gyraseb 24KDA in complex with kibdelomycin

4URM · DNA gyrase subunit B: “Crystal structure of staph gyraseb 24KDA in complex with kibdelomycin”. X-ray diffraction, 1 ligand (XAM), 8 pockets (best druggability 0.77). MolNFT v1 #107934 on GenesisL1: 3D structure, binding sites and…

PDB: 4URM
Type: protein
Length: 770 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA gyrase subunit B
EC: 5.99.1.3
UniProt: P0A0K8
Ligands: XAM
Pockets: 8 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA gyrase subunit B (EC 5.99.1.3)	protein	194	28% helix, 31% strand	P0A0K8
B	DNA gyrase subunit B (EC 5.99.1.3)	protein	195	30% helix, 29% strand	P0A0K8
C	DNA gyrase subunit B (EC 5.99.1.3)	protein	191	29% helix, 32% strand	P0A0K8
D	DNA gyrase subunit B (EC 5.99.1.3)	protein	190	31% helix, 29% strand	P0A0K8

Ligands and binding sites

XAM · (1R,4aS,5S,6S,8aR)-5-{[(5S)-1-(3-O-acetyl-4-O-carbamoyl-6-deoxy-2-O-methyl-alpha-L-talopyranosyl)-4-hydroxy-2-oxo-5-(propan-2-yl)-2,5-dihydro-1H-pyrrol-3-yl]carbonyl}-6-methyl-4-methylidene-1,2,3,4,4a,5,6,8a-octahydronaphthalen-1-yl 2,6-dideoxy-3-C-[(1S)-1-{[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)carbonyl]amino}ethyl]-beta-D-ribo-hexopyranoside · ligand · 4 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	914	0.77	0.80	81	XAM
2	140	0.54	0.81	28	empty
3	175	0.52	0.79	32	empty
4	138	0.52	0.80	23	empty
5	219	0.49	0.76	31	empty

Interfaces

5 interfaces between chains.

A–C · 564 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 337 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 224 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 139 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 21 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4URM · Crystal Structure of Staph GyraseB 24kDa in complex with Kibdelomycin · the same entry in another collection · chain D against D, TM-score 1.00
P0A0K8 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0A0K8) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P0A0K8
Elsewhere: RCSB PDB 4URM · PDBe 4URM · UniProt P0A0K8

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