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Crystal structure of organophosphate ANHYDROLASE/PROLIDASE

Analyse Crystal structure of organophosphate ANHYDROLASE/PROLIDASE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3L7G
Type: protein
Length: 1,259 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xaa-pro dipeptidase
EC: 3.4.13.9, 3.1.8.2, 3.1.8.1
UniProt: Q44238
Ligands: M44, MN
Pockets: 17 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Xaa-pro dipeptidase (EC 3.4.13.9, 3.1.8.2, 3.1.8.1)	protein	425	40% helix, 17% strand	Q44238
B, C	Xaa-pro dipeptidase (EC 3.4.13.9, 3.1.8.2, 3.1.8.1)	protein	417	41% helix, 17% strand	Q44238

Ligands and binding sites

M44 · N,N'-bis(1-methylethyl)phosphorodiamidic acid · ligand · 3 copies · chains A, B, C
MN · Manganese (II) ion · metal · 11 copies · chains A, B, C

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

Pockets

17 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1034	0.69	0.74	102	empty
2	462	0.59	0.74	53	empty
3	227	0.48	0.75	27	empty
4	139	0.45	0.77	22	empty
5	152	0.45	0.76	19	empty

Interfaces

3 interfaces between chains.

A–B · 487 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 454 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 283 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3L7G · Crystal structure of organophosphate anhydrolase/prolidase · the same entry in another collection · chain A against A, TM-score 1.00
Q44238 · AlphaFold monomer V2.0 prediction for xaa-pro dipeptidase (Q44238) · a predicted model of the same protein · chain B 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 Q44238
Elsewhere: RCSB PDB 3L7G · PDBe 3L7G · UniProt Q44238

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