Research workbench
Structure of amino acid amide racemase from ochrobactrum anthropi
Analyse Structure of amino acid amide racemase from ochrobactrum anthropi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GIO
- Type
- protein
- Length
- 1,738 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amino acid amide racemase
- UniProt
- Q06K28
- Ligands
- PLP
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Amino acid amide racemase | protein | 434 | 40% helix, 19% strand | Q06K28 |
| A | Amino acid amide racemase | protein | 433 | 40% helix, 18% strand | Q06K28 |
| B | Amino acid amide racemase | protein | 435 | 40% helix, 18% strand | Q06K28 |
| C | Amino acid amide racemase | protein | 436 | 41% helix, 18% strand | Q06K28 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains D, B, A, C
- EDO · 1,2-ethanediol · additive · chains D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.81 | 0.96 | 28 | empty |
| 2 | 165 | 0.81 | 0.96 | 28 | empty |
| 3 | 468 | 0.76 | 0.84 | 71 | PLP |
| 4 | 453 | 0.74 | 0.84 | 63 | PLP |
| 5 | 442 | 0.74 | 0.83 | 66 | PLP |
Interfaces
4 interfaces between chains.
- A–C · 4263 Ų buried · 84 hydrogen bonds · protein-protein
- D–B · 4246 Ų buried · 75 hydrogen bonds · protein-protein
- D–C · 1264 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1238 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6GIO · Structure of Amino Acid Amide Racemase from Ochrobactrum anthropi · the same entry in another collection · chain D against D, 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 Q06K28
- Elsewhere: RCSB PDB 6GIO · PDBe 6GIO · UniProt Q06K28
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