Research workbench
Chasing acyl carrier protein through a catalytic cycle of lipid a production
Analyse Chasing acyl carrier protein through a catalytic cycle of lipid a production in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IHF
- Type
- protein
- Length
- 2,460 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase; Acyl carrier protein
- EC
- 2.3.1.191
- UniProt
- P21645, G7RM21
- Ligands
- 1F7, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 9 distinct chains · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase (EC 2.3.1.191) | protein | 336 | 17% helix, 30% strand | P21645 |
| B, C | Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase (EC 2.3.1.191) | protein | 336 | 16% helix, 29% strand | P21645 |
| D | Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase (EC 2.3.1.191) | protein | 338 | 17% helix, 29% strand | P21645 |
| G | Acyl carrier protein | protein | 76 | 53% helix, 3% strand | G7RM21 |
| H | Acyl carrier protein | protein | 75 | 49% helix, 3% strand | G7RM21 |
| I | Acyl carrier protein | protein | 73 | 58% helix, 3% strand | G7RM21 |
| J | Acyl carrier protein | protein | 70 | 53% helix, 3% strand | G7RM21 |
| K | Acyl carrier protein | protein | 76 | 51% helix, 3% strand | G7RM21 |
| L | Acyl carrier protein | protein | 72 | 50% helix, 3% strand | G7RM21 |
Ligands and binding sites
- 1F7 · S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (3R)-3-hydroxytetradecanethioate · ligand · 6 copies · chains D, E, F, G, H, A, B, C, I, J, K, L
- CL · Chloride ion · ion · 2 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.78 | 0.96 | 21 | CL |
| 2 | 120 | 0.77 | 0.96 | 21 | CL |
| 3 | 109 | 0.76 | 0.96 | 15 | empty |
| 4 | 114 | 0.76 | 0.96 | 21 | empty |
| 5 | 93 | 0.76 | 0.98 | 45 | empty |
Interfaces
31 interfaces between chains.
- E–F · 3151 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 3147 Ų buried · 39 hydrogen bonds · protein-protein
- D–F · 3145 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 3117 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 3079 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 4IHF · Chasing Acyl Carrier Protein Through a Catalytic Cycle of Lipid A Production · the same entry in another collection · chain L against L, 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 P21645
- Every structure of UniProt G7RM21
- Elsewhere: RCSB PDB 4IHF · PDBe 4IHF · UniProt P21645 · UniProt G7RM21
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