Research workbench
Crystal structure of putative zn-dependent alcohol dehydrogenases from rhodobacter sphaeroides.
Analyse Crystal structure of putative zn-dependent alcohol dehydrogenases from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IV6
- Type
- protein
- Length
- 1,016 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative zn-dependent alcohol dehydrogenase
- UniProt
- Q3IV08
- Ligands
- SAM, CL
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative zn-dependent alcohol dehydrogenase | protein | 257 | 39% helix, 21% strand | Q3IV08 |
| B | Putative zn-dependent alcohol dehydrogenase | protein | 252 | 38% helix, 20% strand | Q3IV08 |
| C | Putative zn-dependent alcohol dehydrogenase | protein | 254 | 42% helix, 21% strand | Q3IV08 |
| D | Putative zn-dependent alcohol dehydrogenase | protein | 253 | 40% helix, 20% strand | Q3IV08 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.79 | 0.92 | 42 | SAM |
| 2 | 212 | 0.79 | 0.93 | 41 | SAM |
| 3 | 1169 | 0.78 | 0.80 | 114 | empty |
| 4 | 743 | 0.74 | 0.79 | 65 | SAM, CL |
| 5 | 619 | 0.73 | 0.80 | 58 | SAM |
Interfaces
5 interfaces between chains.
- C–D · 395 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 394 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 310 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 167 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 136 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 3IV6 · Crystal Structure of Putative Zn-dependent Alcohol Dehydrogenases from Rhodobacter… · the same entry in another collection · chain C against C, 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 Q3IV08
- Elsewhere: RCSB PDB 3IV6 · PDBe 3IV6 · UniProt Q3IV08
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