Research workbench
Crystal structure of AMPDH2 from pseudomonas aeruginosa in complex with pentapeptide
Analyse Crystal structure of AMPDH2 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
- 4BOL
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMPDH2
- UniProt
- Q9HT86
- Ligands
- J0J, ZN
- Pockets
- 6 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | AMPDH2 | protein | 243 | 36% helix, 16% strand | Q9HT86 |
Ligands and binding sites
- J0J · D-alanyl-N-[(2S,6R)-6-amino-6-carboxy-1-{[(1R)-1-carboxyethyl]amino}-1-oxohexan-2-yl]-D-glutamine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.40 | 0.77 | 23 | empty |
| 2 | 51 | 0.35 | 0.79 | 15 | empty |
| 3 | 79 | 0.35 | 0.75 | 21 | ZN |
| 4 | 52 | 0.34 | 0.78 | 13 | empty |
| 5 | 58 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2107 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 4BOL · Crystal structure of AmpDh2 from Pseudomonas aeruginosa in complex with pentapeptide · 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 Q9HT86
- Elsewhere: RCSB PDB 4BOL · PDBe 4BOL · UniProt Q9HT86
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