Research workbench
E.COLI lpxd in complex with compound 7
Analyse E.COLI lpxd in complex with compound 7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P89
- 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, O4A, MG
- Pockets
- 15 · best druggability 0.80
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 | 17% helix, 29% strand | Q0P6M7 |
| B | Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase (EC 2.3.1.191) | protein | 339 | 17% helix, 28% 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 · 2 copies · chains A, B, C
- O4A · N-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-(8-methyl[1]benzopyrano[4,3-c]pyrazol-1(4H)-yl)acetamide · ligand · chains A, B, 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 | 126 | 0.80 | 0.97 | 24 | MG |
| 2 | 99 | 0.76 | 0.97 | 16 | empty |
| 3 | 56 | 0.71 | 0.98 | 20 | empty |
| 4 | 643 | 0.68 | 0.76 | 60 | O4A |
| 5 | 498 | 0.62 | 0.75 | 57 | O3V |
Interfaces
3 interfaces between chains.
- A–B · 3138 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 3111 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 3097 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 6P89 · E.coli LpxD in complex with compound 7 · 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 6P89 · PDBe 6P89 · UniProt Q0P6M7
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