Research workbench
Crystal structure of AMPDH3 from pseudomonas aeruginosa in complex with anhydromuramic pentapeptide
Analyse Crystal structure of AMPDH3 from pseudomonas aeruginosa in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BXE
- Type
- protein
- Length
- 518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMPDH3; Anhydromuramic peptide
- UniProt
- Q9I5D1
- Ligands
- AH0, API
- Pockets
- 5 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | AMPDH3 | protein | 255 | 37% helix, 13% strand | Q9I5D1 |
| C, D | Anhydromuramic peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- AH0 · 2-(2-acetylamino-4-hydroxy-6,8-dioxa-bicyclo[3.2.1]oct-3-yloxy)-propionic acid · ligand · 2 copies · chains A, C, B, D
- API · 2,6-diaminopimelic acid · ligand · 2 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.42 | 0.80 | 15 | empty |
| 2 | 96 | 0.38 | 0.76 | 21 | AH0 |
| 3 | 135 | 0.38 | 0.73 | 28 | API |
| 4 | 96 | 0.37 | 0.75 | 20 | AH0 |
| 5 | 81 | 0.33 | 0.75 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2363 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 314 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 298 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 95 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 68 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 covalent, 6 d-amino (covalent ligand, D-amino acid).
Compared structures
- 4BXE · Crystal structure of AMPDH3 from pseudomonas aeruginosa in complex with anhydromuramic… · 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 Q9I5D1
- Elsewhere: RCSB PDB 4BXE · PDBe 4BXE · UniProt Q9I5D1
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