Research workbench
Crystal structure of the covalent putidaredoxin reductase- putidaredoxin complex
Analyse Crystal structure of the covalent putidaredoxin reductase- putidaredoxin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LB8
- Type
- protein
- Length
- 1,043 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putidaredoxin reductase; Putidaredoxin
- EC
- 1.18.1.-
- UniProt
- P16640, P00259
- Ligands
- FAD, FES
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putidaredoxin reductase (EC 1.18.1.-) | protein | 419 | 26% helix, 29% strand | P16640 |
| B | Putidaredoxin reductase (EC 1.18.1.-) | protein | 417 | 25% helix, 26% strand | P16640 |
| C | Putidaredoxin | protein | 104 | 26% helix, 21% strand | P00259 |
| D | Putidaredoxin | protein | 103 | 13% helix, 17% strand | P00259 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.87 | 0.89 | 121 | FAD |
| 2 | 1199 | 0.80 | 0.82 | 101 | FAD |
| 3 | 656 | 0.80 | 0.85 | 82 | empty |
| 4 | 271 | 0.73 | 0.86 | 49 | empty |
| 5 | 144 | 0.64 | 0.86 | 29 | empty |
Interfaces
4 interfaces between chains.
- A–C · 859 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 846 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 811 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 162 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LB8 · Crystal structure of the covalent putidaredoxin reductase-putidaredoxin complex · the same entry in another collection · chain D against D, TM-score 1.00
- P16640 · AlphaFold monomer V2.0 prediction for putidaredoxin reductase cama (P16640) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P00259 · AlphaFold monomer V2.0 prediction for putidaredoxin (P00259) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P16640
- Every structure of UniProt P00259
- Elsewhere: RCSB PDB 3LB8 · PDBe 3LB8 · UniProt P16640 · UniProt P00259
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