MolNFT v1 · #176917 · protein

Crystal structure of DEHYDROGENASE/ISOMERASE fabx from helicobacter pylori in complex with holo-acp

7E1R · 2-nitropropane dioxygenase: “Crystal structure of DEHYDROGENASE/ISOMERASE fabx from helicobacter pylori in complex with holo-acp”. X-ray diffraction, 3 ligands (FMN, SF4, PN7), 8 pockets (best druggability 0.81). MolNFT v1 #176917…

PDB: 7E1R
Type: protein
Length: 875 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-nitropropane dioxygenase; Acyl carrier PROTEIN,ACYL carrier protein
UniProt: A0A0B2E3F3, A0A0T6M3S8, A0A0B2DUK3
Ligands: FMN, SF4, PN7
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	2-nitropropane dioxygenase	protein	366	39% helix, 16% strand	A0A0B2E3F3
B	Acyl carrier PROTEIN,ACYL carrier protein	protein	71	55% helix, 3% strand	A0A0T6M3S8, A0A0B2DUK3
D	Acyl carrier PROTEIN,ACYL carrier protein	protein	72	58% helix, 3% strand	A0A0T6M3S8, A0A0B2DUK3

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 2 copies · chains A, C
SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, C
PN7 · N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide · ligand · 2 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	944	0.81	0.82	100	FMN, PN7
2	894	0.79	0.82	97	FMN, PN7
3	521	0.69	0.79	56	empty
4	51	0.68	0.96	18	SF4
5	442	0.67	0.79	46	empty

Interfaces

5 interfaces between chains.

A–C · 635 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 451 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 436 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 104 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 84 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

7E1R · Crystal structure of Dehydrogenase/isomerase FabX from Helicobacter pylori in complex… · the same entry in another collection · chain D against D, 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 A0A0B2E3F3
Every structure of UniProt A0A0T6M3S8
Every structure of UniProt A0A0B2DUK3
Elsewhere: RCSB PDB 7E1R · PDBe 7E1R · UniProt A0A0B2E3F3 · UniProt A0A0T6M3S8 · UniProt A0A0B2DUK3

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