MolNFT v1 · #40550 · protein

Crystal structure of human prolidase

2IW2 · Xaa-pro dipeptidase: “Crystal structure of human prolidase”. X-ray diffraction, 1 ligand (NA), 7 pockets (best druggability 0.83). MolNFT v1 #40550 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2IW2
Type: protein
Length: 954 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xaa-pro dipeptidase
EC: 3.4.13.9
UniProt: P12955
Ligands: NA
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Xaa-pro dipeptidase (EC 3.4.13.9)	protein	477	38% helix, 17% strand	P12955

Ligands and binding sites

NA · Sodium ion · metal · 5 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	815	0.83	0.86	66	empty
2	977	0.81	0.82	89	empty
3	904	0.81	0.83	99	empty
4	77	0.45	0.81	23	empty
5	74	0.44	0.81	26	empty

Interfaces

1 interface between chains.

A–B · 3093 Å² buried · 45 hydrogen bonds · protein-protein

Compared structures

2IW2 · Crystal structure of human Prolidase · the same entry in another collection · chain A against A, TM-score 1.00
P12955 · AlphaFold monomer V2.0 prediction for xaa-pro dipeptidase (P12955) · a predicted model of the same protein · 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 P12955
Elsewhere: RCSB PDB 2IW2 · PDBe 2IW2 · UniProt P12955

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