MolNFT v1 · #160018 · protein
E.COLI lpxd in complex with compound 6
6P88 · Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase: “E.COLI lpxd in complex with compound 6”. X-ray diffraction, 3 ligands (O3V, O4G, MG), 15 pockets (best druggability 0.80). MolNFT v1 #160018 on GenesisL1: 3D structure…
- PDB
- 6P88
- Type
- protein
- Length
- 1,011 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase
- EC
- 2.3.1.191
- UniProt
- Q0P6M7
- Ligands
- O3V, O4G, MG
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase (EC 2.3.1.191) | protein | 335 | 17% helix, 30% strand | Q0P6M7 |
| B | Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase (EC 2.3.1.191) | protein | 339 | 16% helix, 29% strand | Q0P6M7 |
| C | Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase (EC 2.3.1.191) | protein | 337 | 17% helix, 30% strand | Q0P6M7 |
Ligands and binding sites
- O3V · 3-hydroxy-7,7-dimethyl-2-phenyl-4-(thiophen-2-yl)-2,6, 7,8-tetrahydro-5H-pyrazolo[3,4-b]quinolin-5-one · ligand · 2 copies · chains A, B, C
- O4G · N-{3-[(furan-2-carbonyl)amino]phenyl}-2,3-dihydro-1,4-benzodioxine-6-carboxamide · ligand · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.80 | 0.98 | 23 | MG |
| 2 | 99 | 0.77 | 0.97 | 15 | empty |
| 3 | 56 | 0.71 | 0.98 | 19 | empty |
| 4 | 631 | 0.67 | 0.76 | 61 | O4G |
| 5 | 523 | 0.63 | 0.76 | 58 | O3V |
Interfaces
3 interfaces between chains.
- A–B · 3136 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 3118 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 3116 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 6P88 · E.coli LpxD in complex with compound 6 · the same entry in another collection · chain A 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 Q0P6M7
- Elsewhere: RCSB PDB 6P88 · PDBe 6P88 · UniProt Q0P6M7
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