Research workbench
Crystal structure of udp-N-acetylglucosamine O-acyltransferase (lpxa) from moraxella catarrhalis RH4.
Analyse Crystal structure of udp-N-acetylglucosamine O-acyltransferase (lpxa) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JXX
- Type
- protein
- Length
- 1,539 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase
- EC
- 2.3.1.129
- UniProt
- D5VAW8
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 257 | 17% helix, 28% strand | D5VAW8 |
| B, E, F | Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 256 | 18% helix, 29% strand | D5VAW8 |
Ligands and binding sites
- GOL · Glycerol · additive · 11 copies · chains A, E, B, C, D, F
- FLC · Citrate anion · additive · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.74 | 0.80 | 92 | GOL |
| 2 | 599 | 0.69 | 0.78 | 65 | GOL |
| 3 | 492 | 0.69 | 0.79 | 61 | GOL |
| 4 | 487 | 0.68 | 0.79 | 58 | FLC |
| 5 | 67 | 0.68 | 0.95 | 22 | empty |
Interfaces
8 interfaces between chains.
- A–E · 1003 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1001 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 950 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 934 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 921 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5JXX · Crystal structure of UDP-N-acetylglucosamine O-acyltransferase (LpxA) from Moraxella… · 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 D5VAW8
- Elsewhere: RCSB PDB 5JXX · PDBe 5JXX · UniProt D5VAW8
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