MolNFT v1 · #160021 · protein
E.COLI lpxd in complex with peptide fitc-RJPXD33
6P8B · Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase: “E.COLI lpxd in complex with peptide fitc-RJPXD33”. X-ray diffraction, 2 ligands (O3V, MG), 13 pockets (best druggability 0.80). MolNFT v1 #160021 on GenesisL1: 3D…
- PDB
- 6P8B
- Type
- protein
- Length
- 1,016 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase; Fitc-RJPXD33
- EC
- 2.3.1.191
- UniProt
- Q0P6M7
- Ligands
- O3V, MG
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 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 | 17% helix, 30% strand | Q0P6M7 |
| C | Udp-3-O-(3-HYDROXYMYRISTOYL)GLUCOSAMINE N-acyltransferase (EC 2.3.1.191) | protein | 337 | 18% helix, 30% strand | Q0P6M7 |
| L | Fitc-RJPXD33 | protein | 5 | 0% helix, 0% strand | — |
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
- 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
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.80 | 0.98 | 23 | MG |
| 2 | 94 | 0.77 | 0.97 | 15 | empty |
| 3 | 455 | 0.71 | 0.81 | 60 | empty |
| 4 | 502 | 0.62 | 0.75 | 58 | O3V |
| 5 | 475 | 0.61 | 0.75 | 57 | O3V |
Interfaces
6 interfaces between chains.
- A–B · 3128 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 3094 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 3051 Ų buried · 35 hydrogen bonds · protein-protein
- C–L · 273 Ų buried · 2 hydrogen bonds · protein-protein
- A–L · 264 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6P8B · E.coli LpxD in complex with peptide FITC-RJPXD33 · 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 6P8B · PDBe 6P8B · UniProt Q0P6M7
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