MolNFT v1 · #38999 · protein
Structure of the ketosynthase-acyltransferase didomain of module 5 from debs.
2HG4 · 6-deoxyerythronolide B synthase: “Structure of the ketosynthase-acyltransferase didomain of module 5 from debs.”. X-ray diffraction, 2 ligands (SO4, CL), 20 pockets (best druggability 0.88). MolNFT v1 #38999 on GenesisL1: 3D…
- PDB
- 2HG4
- Type
- protein
- Length
- 5,281 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-deoxyerythronolide B synthase
- EC
- 2.3.1.94
- UniProt
- Q5UNP4
- Ligands
- SO4, CL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 6-deoxyerythronolide B synthase (EC 2.3.1.94) | protein | 882 | 42% helix, 18% strand | Q5UNP4 |
| D | 6-deoxyerythronolide B synthase (EC 2.3.1.94) | protein | 884 | 39% helix, 18% strand | Q5UNP4 |
| E | 6-deoxyerythronolide B synthase (EC 2.3.1.94) | protein | 877 | 40% helix, 17% strand | Q5UNP4 |
| F | 6-deoxyerythronolide B synthase (EC 2.3.1.94) | protein | 874 | 40% helix, 18% strand | Q5UNP4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, E, F
- CL · Chloride ion · ion · 5 copies · chains B, C, D, E, F
- ACT · Acetate ion · additive · 6 copies · chains A, B, C, D, E, F
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 | 1171 | 0.88 | 0.90 | 123 | empty |
| 2 | 1157 | 0.88 | 0.90 | 124 | empty |
| 3 | 1190 | 0.88 | 0.89 | 126 | empty |
| 4 | 1113 | 0.75 | 0.78 | 92 | empty |
| 5 | 318 | 0.68 | 0.82 | 44 | ACT |
Interfaces
7 interfaces between chains.
- C–D · 2932 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2886 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 2685 Ų buried · 30 hydrogen bonds · protein-protein
- C–F · 419 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 336 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 91 modified, 1 covalent (engineered, additive adduct).
Compared structures
- 2HG4 · Structure of the ketosynthase-acyltransferase didomain of module 5 from DEBS. · the same entry in another collection · chain B against B, 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 Q5UNP4
- Elsewhere: RCSB PDB 2HG4 · PDBe 2HG4 · UniProt Q5UNP4
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