Research workbench
Crystal structure of CHMS Dehydrogenase PmdC from Comamonas testosteroni bound to cofactor NADP
Analyse Crystal structure of CHMS Dehydrogenase PmdC from Comamonas testosteroni bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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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