Research workbench
Alcohol dehydrogenase adh-'a' from rhodococcus ruber dsm 44541 at pH 8.5 in complex with NAD and butane-1,4-diol
Analyse Alcohol dehydrogenase adh-'a' from rhodococcus ruber dsm 44541 at pH 8.5 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XAA
- Type
- protein
- Length
- 1,364 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secondary alcohol dehydrogenase
- EC
- 1.1.1.1
- UniProt
- Q8KLT9
- Ligands
- NAD, ZN
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Secondary alcohol dehydrogenase (EC 1.1.1.1) | protein | 333 | 32% helix, 21% strand | Q8KLT9 |
| B | Secondary alcohol dehydrogenase (EC 1.1.1.1) | protein | 342 | 27% helix, 24% strand | Q8KLT9 |
| C | Secondary alcohol dehydrogenase (EC 1.1.1.1) | protein | 344 | 30% helix, 25% strand | Q8KLT9 |
| D | Secondary alcohol dehydrogenase (EC 1.1.1.1) | protein | 345 | 30% helix, 26% strand | Q8KLT9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- BU1 · 1,4-butanediol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.78 | 0.81 | 71 | NAD |
| 2 | 710 | 0.77 | 0.82 | 61 | NAD, BU1 |
| 3 | 530 | 0.77 | 0.84 | 54 | NAD, BU1 |
| 4 | 792 | 0.76 | 0.80 | 73 | NAD, BU1 |
| 5 | 457 | 0.74 | 0.83 | 90 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1440 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1439 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 474 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 466 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 454 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2XAA · Alcohol dehydrogenase ADH-'A' from Rhodococcus ruber DSM 44541 at pH 8.5 in complex with… · 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 Q8KLT9
- Elsewhere: RCSB PDB 2XAA · PDBe 2XAA · UniProt Q8KLT9
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