MolNFT v1 · #16801 · protein

Crystal structure of the S131A mutant of malonamidase E2 complexed with malonate from bradyrhizobium japonicum

1O9P: “Crystal structure of the S131A mutant of malonamidase E2 complexed with malonate from bradyrhizobium japonicum”. X-ray diffraction, 7 pockets (best druggability 0.87). MolNFT v1 #16801 on GenesisL1: 3D structure, binding sites and…

PDB: 1O9P
Type: protein
Length: 824 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Malonamidase E2
UniProt: Q9ZIV5
Pockets: 7 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Malonamidase E2	protein	412	43% helix, 17% strand	Q9ZIV5

Ligands and binding sites

MLA · Malonic acid · additive · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	472	0.87	0.94	58	empty
2	944	0.75	0.78	83	empty
3	139	0.54	0.81	29	empty
4	150	0.52	0.80	22	MLA
5	78	0.31	0.73	19	empty

Interfaces

1 interface between chains.

A–B · 1570 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

1O9P · Crystal structure of the S131A mutant of Malonamidase E2 complexed with malonate 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 Q9ZIV5
Elsewhere: RCSB PDB 1O9P · PDBe 1O9P · UniProt Q9ZIV5

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