MolNFT v2 · #226666 · protein
Crystal structure of CHMS Dehydrogenase PmdC from Comamonas testosteroni bound to cofactor NADP
9AZO: “Crystal structure of CHMS Dehydrogenase PmdC from Comamonas testosteroni bound to cofactor NADP”. X-ray diffraction at 2.34, 2 ligands (NAP, SO4), 17 pockets (best druggability 0.80). MolNFT v2 #226666 on GenesisL1: 3D structure…
- PDB
- 9AZO
- Type
- protein
- Length
- 1,890 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.34
- Source
- Comamonas testosteroni ATCC 11996
- Molecule
- PmdC
- EC
- 1.-.-.-
- UniProt
- Q93PS4
- Ligands
- NAP, SO4
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.34 · 1 distinct chain · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | PmdC (EC 1.-.-.-) | protein | 315 | 37% helix, 28% strand | Q93PS4 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.80 | 0.82 | 94 | SO4, NAP |
| 2 | 969 | 0.77 | 0.79 | 92 | SO4, NAP |
| 3 | 574 | 0.76 | 0.83 | 56 | SO4, NAP |
| 4 | 569 | 0.75 | 0.82 | 55 | SO4, NAP |
| 5 | 564 | 0.73 | 0.81 | 54 | SO4, NAP |
Interfaces
9 interfaces between chains.
- C–D · 1464 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1443 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1438 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 393 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 351 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
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 Q93PS4
- Elsewhere: RCSB PDB 9AZO · PDBe 9AZO · UniProt Q93PS4
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