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Crystal structure of dipeptide epimerase from cytophaga hutchinsonii complexed with mg and dipeptide D-ala-L-ala
Analyse Crystal structure of dipeptide epimerase from cytophaga hutchinsonii complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q4D
- Type
- protein
- Length
- 3,330 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme family
- EC
- 5.5.1.7
- UniProt
- Q11T61
- Ligands
- MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I | Mandelate RACEMASE/MUCONATE lactonizing enzyme family (EC 5.5.1.7) | protein | 370 | 40% helix, 26% strand | Q11T61 |
Ligands and binding sites
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D, E, F, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.82 | 0.83 | 88 | empty |
| 2 | 1094 | 0.78 | 0.80 | 95 | empty |
| 3 | 143 | 0.61 | 0.85 | 26 | empty |
| 4 | 333 | 0.61 | 0.78 | 53 | empty |
| 5 | 150 | 0.59 | 0.84 | 26 | empty |
Interfaces
11 interfaces between chains.
- B–E · 1010 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 779 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 768 Ų buried · 4 hydrogen bonds · protein-protein
- A–G · 483 Ų buried · 7 hydrogen bonds · protein-protein
- C–H · 468 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 d-amino (D-amino acid).
Compared structures
- 3Q4D · Crystal structure of dipeptide epimerase from Cytophaga hutchinsonii complexed with Mg… · the same entry in another collection · chain I against I, TM-score 1.00
- Q11T61 · AlphaFold monomer V2.0 prediction for D-ala-D/L-ala epimerase (Q11T61) · a predicted model of the same protein · chain F 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 Q11T61
- Elsewhere: RCSB PDB 3Q4D · PDBe 3Q4D · UniProt Q11T61
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