MolNFT v1 · #60016 · protein

Crystal structure of (3R)-hydroxyacyl-acyl carrier protein dehydratase (fabz) from helicobacter pylori in complex with apigenin

3CF9 · (3R)-hydroxymyristoyl-acyl carrier protein dehydratase: “Crystal structure of (3R)-hydroxyacyl-acyl carrier protein dehydratase (fabz) from helicobacter pylori in…”. X-ray diffraction, 3 ligands (BEN, AGI, CL), 12 pockets (best…

PDB: 3CF9
Type: protein
Length: 901 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: (3R)-hydroxymyristoyl-acyl carrier protein dehydratase
EC: 4.2.1.-
UniProt: Q5G940
Ligands: BEN, AGI, CL
Pockets: 12 · best druggability 0.77

Structure

x-ray diffraction · 5 distinct chains · 24% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	(3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-)	protein	152	24% helix, 41% strand	Q5G940
B	(3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-)	protein	149	24% helix, 42% strand	Q5G940
C	(3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-)	protein	150	24% helix, 43% strand	Q5G940
E	(3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-)	protein	151	24% helix, 43% strand	Q5G940
F	(3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-)	protein	147	24% helix, 41% strand	Q5G940

Ligands and binding sites

BEN · Benzamidine · ligand · 4 copies · chains B, C, E
AGI · 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one · ligand · 2 copies · chains A, B, C, D
CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F

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

Pockets

12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	291	0.77	0.88	36	AGI, CL
2	1012	0.76	0.78	77	empty
3	380	0.74	0.85	44	CL, AGI, BEN
4	62	0.73	0.98	18	empty
5	176	0.72	0.89	37	CL

Interfaces

6 interfaces between chains.

E–F · 1456 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1395 Å² buried · 15 hydrogen bonds · protein-protein
C–E · 1281 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1276 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 1276 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

3CF9 · Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from… · 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 Q5G940
Elsewhere: RCSB PDB 3CF9 · PDBe 3CF9 · UniProt Q5G940

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