MolNFT v1 · #105922 · protein
Acetolactate synthase from bacillus subtilis bound to lthdp - crystal form II
4RJK: “Acetolactate synthase from bacillus subtilis bound to lthdp - crystal form II”. X-ray diffraction, 4 ligands (TPP, PYR, TDL), 20 pockets (best druggability 0.82). MolNFT v1 #105922 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4RJK
- Type
- protein
- Length
- 4,410 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetolactate synthase
- EC
- 4.1.3.18
- UniProt
- V5MX36
- Ligands
- TPP, PYR, TDL, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Acetolactate synthase (EC 4.1.3.18) | protein | 552 | 45% helix, 17% strand | V5MX36 |
| B | Acetolactate synthase (EC 4.1.3.18) | protein | 550 | 46% helix, 17% strand | V5MX36 |
| C | Acetolactate synthase (EC 4.1.3.18) | protein | 553 | 45% helix, 17% strand | V5MX36 |
| D | Acetolactate synthase (EC 4.1.3.18) | protein | 550 | 46% helix, 17% strand | V5MX36 |
| G | Acetolactate synthase (EC 4.1.3.18) | protein | 553 | 45% helix, 17% strand | V5MX36 |
| H | Acetolactate synthase (EC 4.1.3.18) | protein | 548 | 44% helix, 17% strand | V5MX36 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 7 copies · chains A, B, C, D, E, F, G, H
- PYR · Pyruvic acid · ligand · 5 copies · chains E, F, G, H
- TDL · 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-(1-carboxy-1-hydroxyethyl)-5-(2-{[hydroxy(phosphonooxy) phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium · ligand · chains G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- PG4 · Tetraethylene glycol · additive · 42 copies · chains A, B, D, C, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.82 | 0.87 | 103 | empty |
| 2 | 830 | 0.81 | 0.84 | 103 | PG4 |
| 3 | 581 | 0.81 | 0.87 | 77 | PG4 |
| 4 | 478 | 0.78 | 0.86 | 61 | TPP, MG |
| 5 | 462 | 0.78 | 0.86 | 61 | TPP, MG |
Interfaces
11 interfaces between chains.
- G–H · 3693 Ų buried · 70 hydrogen bonds · protein-protein
- A–B · 3669 Ų buried · 69 hydrogen bonds · protein-protein
- E–F · 3660 Ų buried · 68 hydrogen bonds · protein-protein
- C–D · 3654 Ų buried · 72 hydrogen bonds · protein-protein
- A–D · 1324 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 4RJK · Acetolactate synthase from Bacillus subtilis bound to LThDP - crystal form II · 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 V5MX36
- Elsewhere: RCSB PDB 4RJK · PDBe 4RJK · UniProt V5MX36
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