Research workbench
Crystal structure of carveol dehydrogenase from mycobacterium avium in complex with NAD
Analyse Crystal structure of carveol dehydrogenase from mycobacterium avium in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EJ2
- Type
- protein
- Length
- 1,108 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carveol dehydrogenase
- EC
- 1.1.1.275
- UniProt
- A0A0H2ZYS9
- Ligands
- NAD, PO4
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Carveol dehydrogenase (EC 1.1.1.275) | protein | 277 | 48% helix, 15% strand | A0A0H2ZYS9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B, C, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.84 | 0.90 | 61 | NAD, MPD |
| 2 | 534 | 0.84 | 0.90 | 64 | NAD, MPD |
| 3 | 585 | 0.83 | 0.88 | 60 | NAD, MPD |
| 4 | 786 | 0.82 | 0.85 | 87 | NAD, MPD |
| 5 | 70 | 0.43 | 0.81 | 17 | PO4 |
Interfaces
3 interfaces between chains.
- A–B · 1566 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1542 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 290 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5EJ2 · Crystal structure of Carveol dehydrogenase from Mycobacterium avium in complex with NAD · 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 A0A0H2ZYS9
- Elsewhere: RCSB PDB 5EJ2 · PDBe 5EJ2 · UniProt A0A0H2ZYS9
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