Research workbench
Crystal structure of wild-type human prolidase with glypro ligand
Analyse Crystal structure of wild-type human prolidase with glypro ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M4J
- Type
- protein
- Length
- 972 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
- 9 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 486 | 37% helix, 17% strand | P12955 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.83 | 0.86 | 70 | empty |
| 2 | 841 | 0.79 | 0.82 | 94 | GOL |
| 3 | 867 | 0.78 | 0.81 | 95 | GOL |
| 4 | 157 | 0.46 | 0.76 | 19 | empty |
| 5 | 66 | 0.44 | 0.82 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 3200 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
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 5M4J · PDBe 5M4J · UniProt P12955
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