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
- 4IHH
- Type
- protein
- Length
- 2,336 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
- PNS
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 10 distinct chains · 22% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase (EC 2.3.1.191) | protein | 337 | 17% helix, 29% strand | P21645 |
| B, D | Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase (EC 2.3.1.191) | protein | 335 | 17% helix, 29% strand | P21645 |
| C | Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase (EC 2.3.1.191) | protein | 337 | 16% helix, 29% strand | P21645 |
| E | Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase (EC 2.3.1.191) | protein | 340 | 16% helix, 30% strand | P21645 |
| F | Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase (EC 2.3.1.191) | protein | 338 | 16% helix, 30% strand | P21645 |
| G | Acyl carrier protein | protein | 70 | 51% helix, 3% strand | G7RM21 |
| H, L | Acyl carrier protein | protein | 10 | 60% helix, 0% strand | G7RM21 |
| I | Acyl carrier protein | protein | 75 | 52% helix, 3% strand | G7RM21 |
| J | Acyl carrier protein | protein | 76 | 54% helix, 3% strand | G7RM21 |
| K | Acyl carrier protein | protein | 73 | 52% helix, 3% strand | G7RM21 |
Ligands and binding sites
- PNS · 4'-phosphopantetheine · ligand · 6 copies · chains A, B, C, G, H, D, E, F, I, J, K, L
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 7 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.78 | 0.97 | 21 | empty |
| 2 | 106 | 0.78 | 0.97 | 19 | empty |
| 3 | 111 | 0.78 | 0.97 | 17 | empty |
| 4 | 91 | 0.76 | 0.98 | 39 | empty |
| 5 | 104 | 0.76 | 0.96 | 16 | empty |
Interfaces
28 interfaces between chains.
- D–E · 3182 Ų buried · 37 hydrogen bonds · protein-protein
- D–F · 3157 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 3147 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 3146 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3143 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (phosphopantetheinylation).
Compared structures
- 4IHH · 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 4IHH · PDBe 4IHH · UniProt P21645 · UniProt G7RM21
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