MolNFT v1 · #108675 · protein
Crystal structure of a short chain dehydrogenase from mycobacterium smegmatis
4WEC: “Crystal structure of a short chain dehydrogenase from mycobacterium smegmatis”. X-ray diffraction, 3 ligands (NAD, MG, ZN), 9 pockets (best druggability 0.87). MolNFT v1 #108675 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4WEC
- Type
- protein
- Length
- 1,023 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short chain dehydrogenase
- UniProt
- A0QVJ7
- Ligands
- NAD, MG, ZN
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Short chain dehydrogenase | protein | 258 | 50% helix, 16% strand | A0QVJ7 |
| B | Short chain dehydrogenase | protein | 254 | 50% helix, 16% strand | A0QVJ7 |
| C | Short chain dehydrogenase | protein | 253 | 50% helix, 16% strand | A0QVJ7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.87 | 0.90 | 83 | EDO |
| 2 | 601 | 0.70 | 0.78 | 53 | NAD, EDO |
| 3 | 586 | 0.69 | 0.78 | 48 | NAD |
| 4 | 537 | 0.67 | 0.77 | 45 | NAD |
| 5 | 514 | 0.66 | 0.77 | 49 | NAD |
Interfaces
6 interfaces between chains.
- B–D · 1761 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1732 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1685 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1671 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 925 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4WEC · Crystal structure of a Short chain dehydrogenase from Mycobacterium smegmatis · 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 A0QVJ7
- Elsewhere: RCSB PDB 4WEC · PDBe 4WEC · UniProt A0QVJ7
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