MolNFT v1 · #103811 · protein

E. COLI gyrb 43-kda N-terminal fragment in complex with ADP

4PRV: “E. COLI gyrb 43-kda N-terminal fragment in complex with ADP”. X-ray diffraction, 2 ligands (ADP, MG), 3 pockets (best druggability 0.72). MolNFT v1 #103811 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PRV
Type: protein
Length: 369 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gyrb
EC: 5.99.1.3
UniProt: P0AES6
Ligands: ADP, MG
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gyrb (EC 5.99.1.3)	protein	369	36% helix, 25% strand	P0AES6

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	238	0.72	0.87	40	ADP, MG
2	224	0.53	0.77	26	empty
3	87	0.38	0.76	16	empty

Compared structures

4PRV · E. coli GyrB 43-kDa N-terminal fragment in complex with ADP · the same entry in another collection · chain A against A, TM-score 1.00
P0AES6 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0AES6) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P0AES6
Elsewhere: RCSB PDB 4PRV · PDBe 4PRV · UniProt P0AES6

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