Research workbench
Crystal structure of the H286K mutant of ferredoxin-NADP+ reductase from plasmodium falciparum in complex with 2'P-AMP
Analyse Crystal structure of the H286K mutant of ferredoxin-NADP+ reductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JQQ
- Type
- protein
- Length
- 1,565 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferredoxin NADP reductase
- EC
- 1.18.1.2
- UniProt
- C6KT68
- Ligands
- FAD, A2P
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferredoxin NADP reductase (EC 1.18.1.2) | protein | 261 | 29% helix, 29% strand | C6KT68 |
| B | Ferredoxin NADP reductase (EC 1.18.1.2) | protein | 263 | 26% helix, 29% strand | C6KT68 |
| C | Ferredoxin NADP reductase (EC 1.18.1.2) | protein | 267 | 28% helix, 27% strand | C6KT68 |
| D | Ferredoxin NADP reductase (EC 1.18.1.2) | protein | 267 | 28% helix, 29% strand | C6KT68 |
| E | Ferredoxin NADP reductase (EC 1.18.1.2) | protein | 253 | 23% helix, 29% strand | C6KT68 |
| F | Ferredoxin NADP reductase (EC 1.18.1.2) | protein | 254 | 24% helix, 29% strand | C6KT68 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- A2P · Adenosine-2'-5'-diphosphate · ligand · 6 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.86 | 0.86 | 105 | FAD, A2P |
| 2 | 996 | 0.85 | 0.86 | 97 | FAD, A2P |
| 3 | 1090 | 0.85 | 0.86 | 103 | FAD, A2P |
| 4 | 455 | 0.68 | 0.80 | 55 | empty |
| 5 | 180 | 0.51 | 0.78 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1256 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1020 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 947 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 603 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 449 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3JQQ · Crystal structure of the H286K mutant of Ferredoxin-NADP+ reductase from Plasmodium… · the same entry in another collection · chain F against F, TM-score 1.00
- C6KT68 · AlphaFold monomer V2.0 prediction for ferredoxin--NADP reductase, apicoplast (C6KT68) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 C6KT68
- Elsewhere: RCSB PDB 3JQQ · PDBe 3JQQ · UniProt C6KT68
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