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

Analyse Crystal structure of the S131A mutant of malonamidase E2 complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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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