Research workbench
Short chain alcohol dehydrogenase from ralstonia sp. dsm 6428 in complex with NADPH
Analyse Short chain alcohol dehydrogenase from ralstonia sp. dsm 6428 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BMS
- Type
- protein
- Length
- 1,487 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alclohol DEHYDROGENASE/SHORT-chain dehydrogenase
- EC
- 1.1.1.1
- UniProt
- C0IR58
- Ligands
- NAP
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alclohol DEHYDROGENASE/SHORT-chain dehydrogenase (EC 1.1.1.1) | protein | 247 | 47% helix, 19% strand | C0IR58 |
| B | Alclohol DEHYDROGENASE/SHORT-chain dehydrogenase (EC 1.1.1.1) | protein | 248 | 48% helix, 19% strand | C0IR58 |
| C | Alclohol DEHYDROGENASE/SHORT-chain dehydrogenase (EC 1.1.1.1) | protein | 248 | 48% helix, 19% strand | C0IR58 |
| E | Alclohol DEHYDROGENASE/SHORT-chain dehydrogenase (EC 1.1.1.1) | protein | 247 | 47% helix, 19% strand | C0IR58 |
| F | Alclohol DEHYDROGENASE/SHORT-chain dehydrogenase (EC 1.1.1.1) | protein | 249 | 47% helix, 19% strand | C0IR58 |
| K | Alclohol DEHYDROGENASE/SHORT-chain dehydrogenase (EC 1.1.1.1) | protein | 248 | 48% helix, 19% strand | C0IR58 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, E, F, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.84 | 0.86 | 73 | empty |
| 2 | 429 | 0.80 | 0.88 | 47 | NAP |
| 3 | 492 | 0.79 | 0.86 | 53 | NAP |
| 4 | 476 | 0.78 | 0.86 | 50 | NAP |
| 5 | 553 | 0.78 | 0.85 | 58 | NAP |
Interfaces
9 interfaces between chains.
- B–C · 1638 Ų buried · 27 hydrogen bonds · protein-protein
- A–F · 1631 Ų buried · 27 hydrogen bonds · protein-protein
- E–K · 1625 Ų buried · 27 hydrogen bonds · protein-protein
- C–F · 1540 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1533 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4BMS · Short chain alcohol dehydrogenase from Ralstonia sp. DSM 6428 in complex with NADPH · 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 C0IR58
- Elsewhere: RCSB PDB 4BMS · PDBe 4BMS · UniProt C0IR58
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