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The crystal structure of malonamidase E2 complexed with malonate from bradyrhizobium japonicum

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

PDB: 1OCL
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: 6 · best druggability 0.86

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

6 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	449	0.86	0.94	57	empty
2	1066	0.76	0.78	101	empty
3	185	0.57	0.81	26	MLA
4	68	0.31	0.74	18	empty
5	79	0.29	0.72	20	empty

Interfaces

1 interface between chains.

A–B · 1572 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

1OCL · The crystal structure of malonamidase E2 complexed with malonate from bradyrhizobium… · 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 1OCL · PDBe 1OCL · UniProt Q9ZIV5

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