MolNFT v1 · #77566 · protein
Crystal structure of dipeptide epimerase from methylococcus capsulatus complexed with mg and dipeptide L-arg-D-lys
3RIT: “Crystal structure of dipeptide epimerase from methylococcus capsulatus complexed with mg and dipeptide…”. X-ray diffraction, 2 ligands (MG, SO4), 17 pockets (best druggability 0.85). MolNFT v1 #77566 on GenesisL1: 3D structure…
- PDB
- 3RIT
- Type
- protein
- Length
- 1,780 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptide epimerase
- UniProt
- Q607C7
- Ligands
- MG, SO4
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Dipeptide epimerase | protein | 356 | 39% helix, 23% strand | Q607C7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 25 copies · chains A, C, B, D, E
- 1PE · Pentaethylene glycol · additive · 4 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.85 | 0.90 | 60 | SO4 |
| 2 | 595 | 0.85 | 0.90 | 63 | SO4 |
| 3 | 576 | 0.76 | 0.83 | 66 | SO4 |
| 4 | 519 | 0.61 | 0.75 | 50 | SO4 |
| 5 | 273 | 0.61 | 0.80 | 31 | SO4 |
Interfaces
6 interfaces between chains.
- D–E · 1205 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1192 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 411 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 230 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 199 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 d-amino (D-amino acid).
Compared structures
- 3RIT · Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg… · the same entry in another collection · chain A against A, TM-score 1.00
- Q607C7 · AlphaFold monomer V2.0 prediction for L-lys-D/L-arg epimerase (Q607C7) · 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 Q607C7
- Elsewhere: RCSB PDB 3RIT · PDBe 3RIT · UniProt Q607C7
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