MolNFT v1 · #115401 · protein

Crystal structure of xaa-pro dipeptidase from xanthomonas campestris in citrate condition

5CIK · Proline dipeptidase: “Crystal structure of xaa-pro dipeptidase from xanthomonas campestris in citrate condition”. X-ray diffraction, 8 pockets (best druggability 0.75). MolNFT v1 #115401 on GenesisL1: 3D structure, binding sites and…

PDB: 5CIK
Type: protein
Length: 794 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proline dipeptidase
EC: 3.4.13.9
UniProt: Q8P839
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Proline dipeptidase (EC 3.4.13.9)	protein	397	36% helix, 22% strand	Q8P839

Ligands and binding sites

CIT · Citric acid · additive · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

8 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	586	0.75	0.82	61	CIT
2	353	0.67	0.81	44	CIT
3	344	0.66	0.80	38	empty
4	97	0.45	0.79	19	empty
5	70	0.34	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 1740 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

5CIK · Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris in citrate condition · 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 Q8P839
Elsewhere: RCSB PDB 5CIK · PDBe 5CIK · UniProt Q8P839

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