MolNFT v1 · #119600 · protein

Pseudomonas aeruginosa hdah bound to pfsaha.

5G11: “Pseudomonas aeruginosa hdah bound to pfsaha.”. X-ray diffraction, 3 ligands (7H1, K, ZN), 5 pockets (best druggability 0.76). MolNFT v1 #119600 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5G11
Type: protein
Length: 744 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hdah
UniProt: Q9HXM1
Ligands: 7H1, K, ZN
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hdah	protein	369	41% helix, 18% strand	Q9HXM1
B	Hdah	protein	375	42% helix, 17% strand	Q9HXM1

Ligands and binding sites

7H1 · 2,2,3,3,4,4,5,5,6,6,7,7-dodecakis(fluoranyl)-~{N}-oxidanyl-~{N}'-phenyl-octanediamide · ligand · 2 copies · chains A, B
K · Potassium ion · metal · 4 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	297	0.76	0.88	46	empty
2	245	0.76	0.89	46	7H1
3	253	0.75	0.88	46	7H1, ZN
4	54	0.34	0.77	12	empty
5	54	0.31	0.76	14	empty

Interfaces

1 interface between chains.

A–B · 2125 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

5G11 · Pseudomonas aeruginosa HDAH bound to PFSAHA. · the same entry in another collection · chain A against A, TM-score 1.00
Q9HXM1 · AlphaFold monomer V2.0 prediction for histone deacetylase-like amidohydrolase (Q9HXM1) · a predicted model of the same protein · chain A 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 Q9HXM1
Elsewhere: RCSB PDB 5G11 · PDBe 5G11 · UniProt Q9HXM1

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