Research workbench
Structure of lpxd from acinetobacter baumannii at 2.66A resolution (P4322 form)
Analyse Structure of lpxd from acinetobacter baumannii at 2.66A resolution (P4322 form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E79
- Type
- protein
- Length
- 1,044 residues
- Chains
- 3
- 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
- 9 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-acylglucosamine N-acyltransferase (EC 2.3.1.-) | protein | 346 | 16% helix, 28% strand | B0VMV2 |
| B | Udp-3-O-acylglucosamine N-acyltransferase (EC 2.3.1.-) | protein | 350 | 19% helix, 28% strand | B0VMV2 |
| C | Udp-3-O-acylglucosamine N-acyltransferase (EC 2.3.1.-) | protein | 348 | 18% helix, 29% strand | B0VMV2 |
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.82 | 0.83 | 143 | empty |
| 2 | 788 | 0.72 | 0.78 | 84 | empty |
| 3 | 54 | 0.69 | 0.96 | 17 | empty |
| 4 | 607 | 0.68 | 0.78 | 68 | empty |
| 5 | 662 | 0.67 | 0.76 | 75 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3191 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 3000 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2989 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 4E79 · Structure of LpxD from Acinetobacter baumannii at 2.66A resolution (P4322 form) · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.97
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 4E79 · PDBe 4E79 · UniProt B0VMV2
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