MolNFT v1 · #86967 · protein
Apo structure of short-chain alcohol dehydrogenase from ralstonia sp. dsm 6428
4BMN · Alclohol DEHYDROGENASE/SHORT-chain dehydrogenase: “Apo structure of short-chain alcohol dehydrogenase from ralstonia sp. dsm 6428”. X-ray diffraction, 1 ligand (TAM), 12 pockets (best druggability 0.83). MolNFT v1 #86967 on…
- PDB
- 4BMN
- Type
- protein
- Length
- 929 residues
- Chains
- 4
- 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
- TAM
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alclohol DEHYDROGENASE/SHORT-chain dehydrogenase (EC 1.1.1.1) | protein | 232 | 45% helix, 20% strand | C0IR58 |
| B | Alclohol DEHYDROGENASE/SHORT-chain dehydrogenase (EC 1.1.1.1) | protein | 231 | 45% helix, 20% strand | C0IR58 |
| C | Alclohol DEHYDROGENASE/SHORT-chain dehydrogenase (EC 1.1.1.1) | protein | 237 | 49% helix, 20% strand | C0IR58 |
| D | Alclohol DEHYDROGENASE/SHORT-chain dehydrogenase (EC 1.1.1.1) | protein | 229 | 47% helix, 21% strand | C0IR58 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains B, C
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.83 | 0.84 | 79 | empty |
| 2 | 392 | 0.61 | 0.77 | 41 | EDO |
| 3 | 236 | 0.56 | 0.78 | 26 | empty |
| 4 | 284 | 0.55 | 0.76 | 42 | EDO |
| 5 | 129 | 0.43 | 0.76 | 19 | TAM |
Interfaces
6 interfaces between chains.
- B–C · 1756 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1620 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1609 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1587 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 166 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4BMN · apo structure of short-chain alcohol dehydrogenase from Ralstonia sp. DSM 6428 · 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 4BMN · PDBe 4BMN · UniProt C0IR58
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