Research workbench
Crystal structure of wild-type human prolidase with mn ions and pro ligand
Analyse Crystal structure of wild-type human prolidase with mn ions and pro ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M4Q
- Type
- protein
- Length
- 962 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
- PRO, MN, OH
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 484 | 38% helix, 18% strand | P12955 |
| B | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 478 | 38% helix, 18% strand | P12955 |
Ligands and binding sites
- PRO · Proline · ligand · 2 copies · chains A, B
- 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
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.83 | 0.86 | 54 | GOL |
| 2 | 913 | 0.81 | 0.83 | 101 | OH, PRO, GOL |
| 3 | 925 | 0.80 | 0.82 | 107 | GOL, MN, OH, PRO |
| 4 | 114 | 0.49 | 0.80 | 16 | empty |
| 5 | 179 | 0.49 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3181 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5M4Q · Crystal Structure of Wild-Type Human Prolidase with Mn ions and Pro ligand · 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 5M4Q · PDBe 5M4Q · UniProt P12955
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