MolNFT v1 · #108227 · protein
The channel-block SER202GLU, THR104LYS double mutant of stearoyl-acp-desaturase from castor bean (ricinus communis)
4V0J · Acyl-[acyl-carrier-protein] desaturase, chloroplastic: “The channel-block SER202GLU, THR104LYS double mutant of stearoyl-acp-desaturase from castor bean (ricinus…”. X-ray diffraction, 1 ligand (FE2), 20 pockets (best druggability…
- PDB
- 4V0J
- Type
- protein
- Length
- 1,961 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-[acyl-carrier-protein] desaturase, chloroplastic
- EC
- 1.14.19.2
- UniProt
- P22337
- Ligands
- FE2
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 69% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-[acyl-carrier-protein] desaturase, chloroplastic (EC 1.14.19.2) | protein | 324 | 70% helix, 2% strand | P22337 |
| B | Acyl-[acyl-carrier-protein] desaturase, chloroplastic (EC 1.14.19.2) | protein | 331 | 70% helix, 2% strand | P22337 |
| C | Acyl-[acyl-carrier-protein] desaturase, chloroplastic (EC 1.14.19.2) | protein | 329 | 69% helix, 2% strand | P22337 |
| D | Acyl-[acyl-carrier-protein] desaturase, chloroplastic (EC 1.14.19.2) | protein | 323 | 69% helix, 2% strand | P22337 |
| E | Acyl-[acyl-carrier-protein] desaturase, chloroplastic (EC 1.14.19.2) | protein | 330 | 70% helix, 2% strand | P22337 |
| F | Acyl-[acyl-carrier-protein] desaturase, chloroplastic (EC 1.14.19.2) | protein | 324 | 69% helix, 2% strand | P22337 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 12 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.79 | 0.98 | 20 | empty |
| 2 | 93 | 0.79 | 0.99 | 20 | empty |
| 3 | 97 | 0.79 | 0.99 | 20 | FE2 |
| 4 | 97 | 0.79 | 0.99 | 20 | empty |
| 5 | 100 | 0.78 | 0.98 | 21 | empty |
Interfaces
9 interfaces between chains.
- C–D · 2681 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2656 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2641 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 629 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 373 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4V0J · The channel-block Ser202Glu, Thr104Lys double mutant of Stearoyl-ACP- Desaturase from… · the same entry in another collection · chain F against F, TM-score 1.00
- P22337 · AlphaFold monomer V2.0 prediction for stearoyl-[acyl-carrier-protein] 9-desaturase… · a predicted model of the same protein · chain F 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 P22337
- Elsewhere: RCSB PDB 4V0J · PDBe 4V0J · UniProt P22337
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