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Crystal structure of Pyrococcus horikoshii quinolinate synthase (NadA) with bound citraconate and Fe4S4 cluster
Analyse Crystal structure of Pyrococcus horikoshii quinolinate synthase (NadA) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KTS
- Type
- protein
- Length
- 303 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.34
- Source
- Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139…
- Molecule
- Quinolinate synthase A
- EC
- 2.5.1.72
- UniProt
- O57767
- Ligands
- SF4, CIZ, CL, NH4
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.34 · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Quinolinate synthase A (EC 2.5.1.72) | protein | 303 | 45% helix, 16% strand | O57767 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- CIZ · (~{Z})-2-methylbut-2-enedioic acid · ligand · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- NH4 · Ammonium ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.77 | 0.97 | 30 | SF4, CIZ, CL |
| 2 | 75 | 0.30 | 0.73 | 20 | empty |
Compared structures
- 5KTS · Crystal structure of pyrococcus horikoshii quinolinate synthase (nada) with bound… · the same entry in another collection · chain A against A, TM-score 1.00
- O57767 · AlphaFold monomer V2.0 prediction for quinolinate synthase a (O57767) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O57767
- Elsewhere: RCSB PDB 5KTS · PDBe 5KTS · UniProt O57767
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