Research workbench
Crystal structure of a putative dehydrogenase (RPA1076) from rhodopseudomonas palustris CGA009 at 2.57 a resolution
Analyse Crystal structure of a putative dehydrogenase (RPA1076) from rhodopseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PM9
- Type
- protein
- Length
- 2,790 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative oxidoreductase
- UniProt
- Q6NAV4
- Ligands
- FAD, UNL, PO4
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Putative oxidoreductase | protein | 465 | 40% helix, 21% strand | Q6NAV4 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- UNL · Unknown ligand · ligand · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 18 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.88 | 0.89 | 136 | empty |
| 2 | 1164 | 0.88 | 0.89 | 131 | empty |
| 3 | 1174 | 0.88 | 0.89 | 141 | empty |
| 4 | 815 | 0.79 | 0.82 | 88 | FAD, UNL, PO4 |
| 5 | 985 | 0.79 | 0.80 | 86 | FAD, UNL, PO4 |
Interfaces
9 interfaces between chains.
- E–F · 3410 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 3379 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 3347 Ų buried · 41 hydrogen bonds · protein-protein
- A–E · 543 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 535 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 3PM9 · Crystal structure of a Putative dehydrogenase (RPA1076) from Rhodopseudomonas palustris… · 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 Q6NAV4
- Elsewhere: RCSB PDB 3PM9 · PDBe 3PM9 · UniProt Q6NAV4
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