MolNFT v1 · #13029 · protein
Mutant enzyme W63Y lumazine synthase from S.POMBE
1KZ4 · 6,7-dimethyl-8-ribityllumazine synthase: “Mutant enzyme W63Y lumazine synthase from S.POMBE”. X-ray diffraction, 1 ligand (PO4), 9 pockets (best druggability 0.78). MolNFT v1 #13029 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1KZ4
- Type
- protein
- Length
- 742 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6,7-dimethyl-8-ribityllumazine synthase
- EC
- 2.5.1.78
- UniProt
- Q9UUB1
- Ligands
- PO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 147 | 52% helix, 21% strand | Q9UUB1 |
| C | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 149 | 53% helix, 21% strand | Q9UUB1 |
| E | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 152 | 51% helix, 20% strand | Q9UUB1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.78 | 0.87 | 50 | empty |
| 2 | 432 | 0.76 | 0.85 | 39 | PO4 |
| 3 | 411 | 0.70 | 0.81 | 35 | PO4 |
| 4 | 395 | 0.70 | 0.81 | 33 | PO4 |
| 5 | 395 | 0.69 | 0.81 | 33 | PO4 |
Interfaces
10 interfaces between chains.
- A–E · 1311 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1150 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1127 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1125 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1116 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1KZ4 · Mutant enzyme W63Y Lumazine Synthase from S.pombe · the same entry in another collection · chain E against E, TM-score 1.00
- Q9UUB1 · AlphaFold monomer V2.0 prediction for 6,7-dimethyl-8-ribityllumazine synthase (Q9UUB1) · a predicted model of the same protein · chain A 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 Q9UUB1
- Elsewhere: RCSB PDB 1KZ4 · PDBe 1KZ4 · UniProt Q9UUB1
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