Research workbench
Structure of rmd from pseudomonas aeruginosa complexed with NADPH
Analyse Structure of rmd from pseudomonas aeruginosa complexed with NADPH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X3B
- Type
- protein
- Length
- 1,178 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-6-deoxy-D-mannose reductase
- UniProt
- A0A071L2P8
- Ligands
- NDP, POP, NO3
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-6-deoxy-D-mannose reductase | protein | 300 | 44% helix, 18% strand | A0A071L2P8 |
| B | GDP-6-deoxy-D-mannose reductase | protein | 297 | 44% helix, 18% strand | A0A071L2P8 |
| C | GDP-6-deoxy-D-mannose reductase | protein | 289 | 45% helix, 17% strand | A0A071L2P8 |
| D | GDP-6-deoxy-D-mannose reductase | protein | 292 | 44% helix, 18% strand | A0A071L2P8 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 5 copies · chains A, B, C, D
- POP · Pyrophosphate 2- · ligand · chains B
- NO3 · Nitrate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.76 | 0.79 | 86 | NDP, POP |
| 2 | 733 | 0.76 | 0.80 | 56 | NDP, NO3 |
| 3 | 710 | 0.73 | 0.79 | 60 | NDP |
| 4 | 714 | 0.73 | 0.79 | 73 | NDP |
| 5 | 307 | 0.70 | 0.84 | 54 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1090 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 1065 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 317 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 35 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6X3B · Structure of RMD from Pseudomonas aeruginosa complexed with NADPH · 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 A0A071L2P8
- Elsewhere: RCSB PDB 6X3B · PDBe 6X3B · UniProt A0A071L2P8
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