Research workbench
Ketoreductase from module 1 of the 6-deoxyerythronolide B synthase (KR1) in complex with antibody fragment (Fab) 1D10
Analyse Ketoreductase from module 1 of the 6-deoxyerythronolide B synthase (KR1) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WH9
- Type
- protein
- Length
- 2,635 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KR1; 1D10 (Fab heavy chain); 1D10 (Fab light chain)
- UniProt
- Q5UNP6
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 9 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | KR1 | protein | 439 | 37% helix, 21% strand | Q5UNP6 |
| E | 1D10 (Fab heavy chain) | protein | 224 | 6% helix, 44% strand | — |
| F | 1D10 (Fab light chain) | protein | 216 | 3% helix, 47% strand | — |
| B | 1D10 (Fab heavy chain) | protein | 225 | 4% helix, 48% strand | — |
| C | 1D10 (Fab light chain) | protein | 215 | 5% helix, 46% strand | — |
| H | 1D10 (Fab heavy chain) | protein | 219 | 5% helix, 49% strand | — |
| I | 1D10 (Fab light chain) | protein | 216 | 6% helix, 49% strand | — |
| D | KR1 | protein | 450 | 36% helix, 20% strand | Q5UNP6 |
| A | KR1 | protein | 431 | 37% helix, 19% strand | Q5UNP6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains G, C, E, F, B, D, I, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.80 | 0.83 | 88 | empty |
| 2 | 1163 | 0.79 | 0.81 | 103 | SO4 |
| 3 | 1076 | 0.79 | 0.80 | 93 | SO4 |
| 4 | 1171 | 0.78 | 0.80 | 99 | SO4 |
| 5 | 917 | 0.77 | 0.80 | 86 | empty |
Interfaces
13 interfaces between chains.
- E–F · 1783 Ų buried · 13 hydrogen bonds · protein-protein
- H–I · 1735 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1630 Ų buried · 17 hydrogen bonds · protein-protein
- I–A · 717 Ų buried · 13 hydrogen bonds · protein-protein
- F–D · 691 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 6WH9 · Ketoreductase from module 1 of the 6-deoxyerythronolide B synthase (KR1) in complex with… · the same entry in another collection · chain F against F, 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 Q5UNP6
- Elsewhere: RCSB PDB 6WH9 · PDBe 6WH9 · UniProt Q5UNP6
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