MolNFT v1 · #97454 · protein
Crosslinked crystal structure of type II fatty synthase dehydratase, faba, and acyl carrier protein, acpp
4KEH · N-{3-[DIHYDROXY(NONYL)-LAMBDA~4~-SULFANYL]PROPYL}-N~3~…: “Crosslinked crystal structure of type II fatty synthase dehydratase, faba, and acyl carrier protein, acpp”. X-ray diffraction, 1 ligand (1R3), 7 pockets (best druggability…
- PDB
- 4KEH
- Type
- protein
- Length
- 485 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-{3-[DIHYDROXY(NONYL)-LAMBDA~4~-SULFANYL]PROPYL}-N~3~…
- EC
- 4.2.1.59, 5.3.3.14
- UniProt
- P0A6Q3, K0BL73
- Ligands
- 1R3
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-{3-[DIHYDROXY(NONYL)-LAMBDA~4~-SULFANYL]PROPYL}-N~3~- [(2R)-2-hydroxy-3,3-dimethyl-4-(PHOSPHONOOXY)BUTANOYL]-beta- alaninamide (EC 4.2.1.59, 5.3.3.14) | protein | 166 | 19% helix, 37% strand | P0A6Q3 |
| B | N-{3-[DIHYDROXY(NONYL)-LAMBDA~4~-SULFANYL]PROPYL}-N~3~- [(2R)-2-hydroxy-3,3-dimethyl-4-(PHOSPHONOOXY)BUTANOYL]-beta- alaninamide (EC 4.2.1.59, 5.3.3.14) | protein | 165 | 19% helix, 38% strand | P0A6Q3 |
| C, D | Acyl carrier protein | protein | 77 | 57% helix, 3% strand | K0BL73 |
Ligands and binding sites
- 1R3 · N-{3-[dihydroxy(nonyl)-lambda~4~-sulfanyl]propyl}-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.73 | 0.87 | 38 | 1R3 |
| 2 | 209 | 0.72 | 0.88 | 36 | 1R3 |
| 3 | 123 | 0.40 | 0.75 | 28 | empty |
| 4 | 63 | 0.39 | 0.79 | 12 | empty |
| 5 | 77 | 0.37 | 0.77 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1451 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 603 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 568 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 65 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4KEH · Crosslinked Crystal Structure of Type II Fatty Synthase Dehydratase, FabA, and Acyl… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6Q3 · AlphaFold monomer V2.0 prediction for 3-hydroxydecanoyl-[acyl- carrier-protein]… · a predicted model of the same protein · chain A 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 P0A6Q3
- Every structure of UniProt K0BL73
- Elsewhere: RCSB PDB 4KEH · PDBe 4KEH · UniProt P0A6Q3 · UniProt K0BL73
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