MolNFT v1 · #121406 · protein
A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase
5HUQ · Lactate racemization operon protein lara: “A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase”. X-ray diffraction, 3 ligands (4EY, NI, SO4), 7 pockets (best druggability 0.82). MolNFT v1 #121406…
- PDB
- 5HUQ
- Type
- protein
- Length
- 865 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate racemization operon protein lara
- UniProt
- A0A0G9FER8
- Ligands
- 4EY, NI, SO4
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactate racemization operon protein lara | protein | 433 | 37% helix, 25% strand | A0A0G9FER8 |
| B | Lactate racemization operon protein lara | protein | 432 | 38% helix, 26% strand | A0A0G9FER8 |
Ligands and binding sites
- 4EY · 3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · chains B
- SO4 · Sulfate ion · ion · 23 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.82 | 0.83 | 114 | 4EY, SO4 |
| 2 | 121 | 0.79 | 0.97 | 30 | NI, 4EY, SO4 |
| 3 | 403 | 0.72 | 0.83 | 69 | SO4 |
| 4 | 531 | 0.69 | 0.79 | 44 | SO4 |
| 5 | 114 | 0.44 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 621 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5HUQ · A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase · 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
- Every structure of UniProt A0A0G9FER8
- Elsewhere: RCSB PDB 5HUQ · PDBe 5HUQ · UniProt A0A0G9FER8
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