Research workbench
Crystal structure of human class II alcohol dehydrogenase (ADH4) in complex with NAD and zn
Analyse Crystal structure of human class II alcohol dehydrogenase (ADH4) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3COS
- Type
- protein
- Length
- 1,518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase 4
- EC
- 1.1.1.1
- UniProt
- P08319
- Ligands
- NAD, ZN
- Pockets
- 10 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Alcohol dehydrogenase 4 (EC 1.1.1.1) | protein | 379 | 28% helix, 26% strand | P08319 |
| D | Alcohol dehydrogenase 4 (EC 1.1.1.1) | protein | 381 | 28% helix, 26% strand | P08319 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.89 | 0.91 | 106 | NAD, ACY |
| 2 | 848 | 0.89 | 0.91 | 109 | NAD, ACY |
| 3 | 142 | 0.69 | 0.90 | 30 | empty |
| 4 | 520 | 0.66 | 0.78 | 51 | EDO |
| 5 | 383 | 0.66 | 0.79 | 44 | EDO |
Interfaces
6 interfaces between chains.
- A–B · 1576 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1565 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 682 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 623 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 343 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3COS · Crystal structure of human class II alcohol dehydrogenase (ADH4) in complex with NAD and… · the same entry in another collection · chain D against D, TM-score 1.00
- P08319 · AlphaFold monomer V2.0 prediction for all-trans-retinol dehydrogenase [NAD(+)] ADH4… · a predicted model of the same protein · chain B 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 P08319
- Elsewhere: RCSB PDB 3COS · PDBe 3COS · UniProt P08319
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