Research workbench
E.COLI lpxd in complex with compound 5
Analyse E.COLI lpxd in complex with compound 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P87
- 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, O4P, MG
- Pockets
- 14 · 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
- O4P · N-[(R)-(1H-indol-3-yl)(thiophen-2-yl)methyl]-2-(2-methoxyphenoxy)-N-methylacetamide · 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
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.80 | 0.98 | 23 | MG |
| 2 | 93 | 0.77 | 0.98 | 40 | empty |
| 3 | 97 | 0.76 | 0.97 | 16 | empty |
| 4 | 647 | 0.67 | 0.76 | 64 | O4P |
| 5 | 497 | 0.63 | 0.75 | 57 | O3V |
Interfaces
3 interfaces between chains.
- A–B · 3125 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 3096 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 3063 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 6P87 · E.coli LpxD in complex with compound 5 · 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 6P87 · PDBe 6P87 · UniProt Q0P6M7
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