Research workbench
Crosslinked crystal structure of type II fatty synthase dehydratase, faba, and acyl carrier protein, acpp
Analyse Crosslinked crystal structure of type II fatty synthase dehydratase, faba, and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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