MolNFT v1 · #68416 · protein
Structure of adh-a from rhodococcus ruber
3JV7: “Structure of adh-a from rhodococcus ruber”. X-ray diffraction, 2 ligands (NAD, ZN), 12 pockets (best druggability 0.81). MolNFT v1 #68416 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3JV7
- Type
- protein
- Length
- 1,380 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adh-a
- EC
- 1.1.1.1
- Ligands
- NAD, ZN
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Adh-a (EC 1.1.1.1) | protein | 345 | 31% helix, 25% strand | — |
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
- ACY · Acetic acid · additive · 4 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.81 | 0.84 | 120 | empty |
| 2 | 701 | 0.77 | 0.82 | 71 | NAD, ACY, MPD |
| 3 | 803 | 0.77 | 0.81 | 74 | NAD, ACY, MPD |
| 4 | 731 | 0.76 | 0.81 | 76 | NAD, ACY, MPD |
| 5 | 733 | 0.76 | 0.80 | 76 | NAD, ACY, MPD |
Interfaces
6 interfaces between chains.
- B–C · 1488 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1473 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 515 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 513 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 456 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3JV7 · Structure of ADH-A from Rhodococcus ruber · 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
- Elsewhere: RCSB PDB 3JV7 · PDBe 3JV7
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