MolNFT v1 · #160014 · protein
E.COLI lpxd in complex with compound 2O
6P84 · Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase: “E.COLI lpxd in complex with compound 2O”. X-ray diffraction, 2 ligands (O3V, MG), 15 pockets (best druggability 0.79). MolNFT v1 #160014 on GenesisL1: 3D structure, binding…
- PDB
- 6P84
- 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, MG
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 29% 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 | 16% helix, 29% strand | Q0P6M7 |
| B | Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase (EC 2.3.1.191) | protein | 339 | 17% helix, 29% strand | Q0P6M7 |
| C | Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase (EC 2.3.1.191) | protein | 337 | 17% helix, 29% 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 · 3 copies · chains A, C, B
- 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 | 115 | 0.79 | 0.98 | 23 | MG |
| 2 | 89 | 0.77 | 0.98 | 42 | empty |
| 3 | 96 | 0.77 | 0.97 | 15 | empty |
| 4 | 639 | 0.68 | 0.76 | 60 | O3V |
| 5 | 520 | 0.63 | 0.75 | 56 | O3V |
Interfaces
3 interfaces between chains.
- A–B · 3143 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 3116 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 3114 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6P84 · E.coli LpxD in complex with compound 2o · 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 6P84 · PDBe 6P84 · UniProt Q0P6M7
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