Research workbench
Crystal structure of human prolidase S202F variant expressed in the presence of chaperones
Analyse Crystal structure of human prolidase S202F variant expressed in the presence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SRE
- Type
- protein
- Length
- 971 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
- MH2, MN
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 486 | 37% helix, 17% strand | P12955 |
| B | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 485 | 37% helix, 17% strand | P12955 |
Ligands and binding sites
- MH2 · Manganese ion, 1 hydroxyl coordinated · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.83 | 0.86 | 73 | empty |
| 2 | 848 | 0.78 | 0.81 | 95 | GOL |
| 3 | 536 | 0.74 | 0.81 | 66 | empty |
| 4 | 308 | 0.64 | 0.80 | 35 | empty |
| 5 | 118 | 0.48 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3182 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 6SRE · Crystal Structure of Human Prolidase S202F variant expressed in the presence of chaperones · 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 6SRE · PDBe 6SRE · UniProt P12955
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