MolNFT v1 · #150736 · protein
Crystal structure of ARG184GLN mutant of human prolidase with mn ions and cacodylate ligand
6H2P · Xaa-pro dipeptidase: “Crystal structure of ARG184GLN mutant of human prolidase with mn ions and cacodylate ligand”. X-ray diffraction, 1 ligand (MN), 9 pockets (best druggability 0.83). MolNFT v1 #150736 on GenesisL1: 3D structure…
- PDB
- 6H2P
- Type
- protein
- Length
- 959 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
- Pockets
- 9 · 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 | 477 | 39% helix, 17% strand | P12955 |
| B | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 482 | 38% helix, 17% strand | P12955 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- CAC · Cacodylate ion · additive · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.83 | 0.85 | 68 | GOL |
| 2 | 1102 | 0.81 | 0.82 | 101 | CAC, GOL |
| 3 | 566 | 0.75 | 0.82 | 70 | GOL |
| 4 | 386 | 0.73 | 0.84 | 44 | CAC |
| 5 | 70 | 0.49 | 0.84 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 3019 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6H2P · Crystal Structure of Arg184Gln mutant of Human Prolidase with Mn ions and Cacodylate… · 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 6H2P · PDBe 6H2P · UniProt P12955
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