MolNFT v1 · #126491 · protein
Crystal structure of wild-type human prolidase with mg ions and leupro ligand
5M4L · Xaa-pro dipeptidase: “Crystal structure of wild-type human prolidase with mg ions and leupro ligand”. X-ray diffraction, 3 ligands (MG, NA, OH), 9 pockets (best druggability 0.83). MolNFT v1 #126491 on GenesisL1: 3D structure…
- PDB
- 5M4L
- 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
- MG, NA, OH
- 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
- MG · Magnesium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · chains 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
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 | 802 | 0.83 | 0.86 | 63 | empty |
| 2 | 786 | 0.77 | 0.81 | 90 | GOL |
| 3 | 827 | 0.77 | 0.81 | 95 | GOL |
| 4 | 159 | 0.46 | 0.76 | 17 | empty |
| 5 | 66 | 0.44 | 0.82 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 3196 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 5M4L · Crystal Structure of Wild-Type Human Prolidase with Mg ions and LeuPro 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 0.98
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 5M4L · PDBe 5M4L · UniProt P12955
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