Research workbench
Histidine racemase from leuconostoc mesenteroides subsp. sake nbrc 102480
Analyse Histidine racemase from leuconostoc mesenteroides subsp. sake nbrc 102480 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZL6
- Type
- protein
- Length
- 1,488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine racemase
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Histidine racemase | protein | 372 | 29% helix, 27% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.89 | 0.92 | 135 | empty |
| 2 | 328 | 0.84 | 0.94 | 69 | empty |
| 3 | 585 | 0.79 | 0.85 | 83 | PLP |
| 4 | 743 | 0.79 | 0.83 | 114 | PLP |
| 5 | 402 | 0.77 | 0.86 | 61 | PLP |
Interfaces
6 interfaces between chains.
- A–B · 2719 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2690 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 937 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 923 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 458 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5ZL6 · Histidine Racemase from Leuconostoc mesenteroides subsp. sake NBRC 102480 · the same entry in another collection · 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
- Elsewhere: RCSB PDB 5ZL6 · PDBe 5ZL6
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