Research workbench
C. trachomatis lpxd
Analyse C. trachomatis lpxd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IUA
- Type
- protein
- Length
- 1,037 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.-
- UniProt
- O84245
- Ligands
- PLM, SO4
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (EC 2.3.1.-) | protein | 346 | 15% helix, 30% strand | O84245 |
| B | Udp-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (EC 2.3.1.-) | protein | 345 | 15% helix, 29% strand | O84245 |
| C | Udp-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (EC 2.3.1.-) | protein | 346 | 15% helix, 29% strand | O84245 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.82 | 0.88 | 49 | PLM |
| 2 | 62 | 0.74 | 0.99 | 30 | empty |
| 3 | 166 | 0.66 | 0.86 | 24 | empty |
| 4 | 301 | 0.65 | 0.81 | 50 | empty |
| 5 | 239 | 0.62 | 0.81 | 37 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2803 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2767 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 2682 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 2IUA · C. trachomatis LpxD · 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 O84245
- Elsewhere: RCSB PDB 2IUA · PDBe 2IUA · UniProt O84245
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