Research workbench
Structure of lpxd from acinetobacter baumannii at 2.85A resolution (P21 form)
Analyse Structure of lpxd from acinetobacter baumannii at 2.85A resolution (P21 form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E75
- Type
- protein
- Length
- 2,022 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-3-O-acylglucosamine N-acyltransferase
- EC
- 2.3.1.-
- UniProt
- B0VMV2
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Udp-3-O-acylglucosamine N-acyltransferase (EC 2.3.1.-) | protein | 337 | 15% helix, 29% strand | B0VMV2 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.80 | 0.83 | 125 | empty |
| 2 | 556 | 0.78 | 0.85 | 82 | empty |
| 3 | 860 | 0.78 | 0.81 | 104 | empty |
| 4 | 751 | 0.71 | 0.77 | 76 | empty |
| 5 | 716 | 0.69 | 0.76 | 72 | empty |
Interfaces
10 interfaces between chains.
- B–C · 2870 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2859 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2854 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2836 Ų buried · 36 hydrogen bonds · protein-protein
- D–F · 2827 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 4E75 · Structure of LpxD from Acinetobacter baumannii at 2.85A resolution (P21 form) · the same entry in another collection · chain B against B, TM-score 1.00
- B0VMV2 · AlphaFold monomer V2.0 prediction for udp-3-O-acylglucosamine N-acyltransferase (B0VMV2) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 B0VMV2
- Elsewhere: RCSB PDB 4E75 · PDBe 4E75 · UniProt B0VMV2
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