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The crystal structure of urdamycin C-6 ketoreductase domain urdmred with bound NADP and rabelomycin
Analyse The crystal structure of urdamycin C-6 ketoreductase domain urdmred with bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OSP
- Type
- protein
- Length
- 1,002 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxygenase-reductase
- UniProt
- K0IB23
- Ligands
- NAP, 2V4
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Oxygenase-reductase | protein | 252 | 50% helix, 15% strand | K0IB23 |
| B | Oxygenase-reductase | protein | 253 | 49% helix, 16% strand | K0IB23 |
| D | Oxygenase-reductase | protein | 245 | 49% helix, 16% strand | K0IB23 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- 2V4 · rabelomycin · ligand · chains A
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 | 1047 | 0.82 | 0.83 | 74 | empty |
| 2 | 554 | 0.73 | 0.81 | 47 | NAP, 2V4 |
| 3 | 568 | 0.71 | 0.79 | 45 | empty |
| 4 | 471 | 0.66 | 0.78 | 48 | empty |
| 5 | 74 | 0.59 | 0.89 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1614 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1567 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1502 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1498 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 212 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4OSP · The crystal structure of urdamycin C-6 ketoreductase domain UrdMred with bound NADP and… · 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 K0IB23
- Elsewhere: RCSB PDB 4OSP · PDBe 4OSP · UniProt K0IB23
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