MolNFT v1 · #61555 · protein

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

3DP3 · (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, 4BB, CL), 11 pockets (best…

PDB: 3DP3
Type: protein
Length: 904 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, 4BB, CL
Pockets: 11 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 24% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	(3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-)	protein	152	24% helix, 42% strand	Q5G940
B, F	(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	151	24% helix, 42% strand	Q5G940
D	(3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-)	protein	151	24% helix, 40% strand	Q5G940

Ligands and binding sites

BEN · Benzamidine · ligand · 6 copies · chains A, B, C, E
4BB · 4-tert-butyl-N'-[(1E)-(3,5-dibromo-2,4-dihydroxyphenyl)methylidene]benzohydrazide · 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

11 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	1023	0.75	0.78	86	empty
2	435	0.74	0.84	50	4BB, CL
3	70	0.72	0.96	20	empty
4	299	0.72	0.85	39	CL, 4BB, BEN
5	73	0.71	0.96	18	empty

Interfaces

6 interfaces between chains.

E–F · 1514 Å² buried · 19 hydrogen bonds · protein-protein
C–E · 1276 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 1240 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1237 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1229 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3DP3 · 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 3DP3 · PDBe 3DP3 · UniProt Q5G940

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.