MolNFT v1 · #126486 · protein

Crystal structure of wild-type human prolidase with mn ions

5M4G · Xaa-pro dipeptidase: “Crystal structure of wild-type human prolidase with mn ions”. X-ray diffraction, 2 ligands (MN, OH), 8 pockets (best druggability 0.83). MolNFT v1 #126486 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5M4G
Type: protein
Length: 964 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: MN, OH
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Xaa-pro dipeptidase (EC 3.4.13.9)	protein	481	38% helix, 16% strand	P12955
B	Xaa-pro dipeptidase (EC 3.4.13.9)	protein	483	38% helix, 17% strand	P12955

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains A, B
OH · Hydroxide ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 7 copies · chains A, B

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	768	0.83	0.86	54	GOL
2	970	0.82	0.83	104	GOL, MN, OH
3	1081	0.81	0.82	104	OH, GOL
4	63	0.46	0.83	24	empty
5	62	0.44	0.82	20	empty

Interfaces

1 interface between chains.

A–B · 2996 Å² buried · 43 hydrogen bonds · protein-protein

Compared structures

5M4G · Crystal Structure of Wild-Type Human Prolidase with Mn ions · 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 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 P12955
Elsewhere: RCSB PDB 5M4G · PDBe 5M4G · UniProt P12955

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