Research workbench
Crystal structure of GLU412LYS mutant of human prolidase with mn ions and glypro ligand
Analyse Crystal structure of GLU412LYS mutant of human prolidase with mn ions and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MC3
- Type
- protein
- Length
- 970 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
- Pockets
- 9 · 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 | 484 | 38% helix, 17% strand | P12955 |
| B | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 486 | 37% helix, 17% strand | P12955 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- OH · Hydroxide ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 10 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 | 789 | 0.83 | 0.86 | 70 | empty |
| 2 | 830 | 0.79 | 0.82 | 97 | NA, GOL |
| 3 | 836 | 0.79 | 0.82 | 97 | empty |
| 4 | 66 | 0.46 | 0.83 | 25 | empty |
| 5 | 59 | 0.43 | 0.82 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3197 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 5MC3 · Crystal Structure of Glu412Lys 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 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 5MC3 · PDBe 5MC3 · UniProt P12955
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