MolNFT v1 · #48658 · protein
Crystal structure of acetoin utilization protein (ZP_00540088.1) from exiguobacterium sibiricum 255-15 at 2.33 a resolution
2Q04: “Crystal structure of acetoin utilization protein (ZP_00540088.1) from exiguobacterium sibiricum 255-15 at…”. X-ray diffraction, 1 ligand (CA), 15 pockets (best druggability 0.80). MolNFT v1 #48658 on GenesisL1: 3D structure, binding…
- PDB
- 2Q04
- Type
- protein
- Length
- 1,250 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetoin utilization protein
- UniProt
- Q41BL0
- Ligands
- CA
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetoin utilization protein | protein | 211 | 37% helix, 25% strand | Q41BL0 |
| B | Acetoin utilization protein | protein | 207 | 37% helix, 25% strand | Q41BL0 |
| C | Acetoin utilization protein | protein | 208 | 36% helix, 25% strand | Q41BL0 |
| D, E | Acetoin utilization protein | protein | 210 | 33% helix, 25% strand | Q41BL0 |
| F | Acetoin utilization protein | protein | 204 | 32% helix, 25% strand | Q41BL0 |
Ligands and binding sites
- CA · Calcium ion · metal · 7 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, C, D, E, F
- ACY · Acetic acid · additive · 4 copies · chains A, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.80 | 0.89 | 80 | empty |
| 2 | 285 | 0.79 | 0.90 | 53 | EDO |
| 3 | 459 | 0.74 | 0.83 | 50 | CA |
| 4 | 688 | 0.73 | 0.79 | 63 | CA |
| 5 | 499 | 0.70 | 0.80 | 50 | CA, EDO |
Interfaces
12 interfaces between chains.
- A–B · 761 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 664 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 642 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 523 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 493 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 modified (engineered).
Compared structures
- 2Q04 · Crystal structure of acetoin utilization protein (ZP_00540088.1) from Exiguobacterium… · 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 Q41BL0
- Elsewhere: RCSB PDB 2Q04 · PDBe 2Q04 · UniProt Q41BL0
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