MolNFT v1 · #126741 · protein
Crystal structure of SER202PHE mutant of human prolidase with mn ions and glypro ligand
5MBZ · Xaa-pro dipeptidase: “Crystal structure of SER202PHE mutant of human prolidase with mn ions and glypro ligand”. X-ray diffraction, 4 ligands (MN, NA, OH), 10 pockets (best druggability 0.85). MolNFT v1 #126741 on GenesisL1: 3D…
- PDB
- 5MBZ
- Type
- protein
- Length
- 963 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, NA, OH, CL
- Pockets
- 10 · best druggability 0.85
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 | 483 | 38% helix, 17% strand | P12955 |
| B | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 480 | 38% helix, 18% strand | P12955 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
- OH · Hydroxide ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.85 | 0.86 | 88 | empty |
| 2 | 737 | 0.75 | 0.80 | 66 | GOL |
| 3 | 568 | 0.74 | 0.81 | 67 | empty |
| 4 | 50 | 0.46 | 0.85 | 17 | empty |
| 5 | 107 | 0.46 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3007 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 5MBZ · Crystal Structure of Ser202Phe mutant of Human Prolidase with Mn ions and GlyPro 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 0.99
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 5MBZ · PDBe 5MBZ · UniProt P12955
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