MolNFT v1 · #87052 · protein
Crystal structure of AMPDH2 from pseudomonas aeruginosa in complex with nag-nam-nag-nam tetrasaccharide
4BPA: “Crystal structure of AMPDH2 from pseudomonas aeruginosa in complex with nag-nam-nag-nam tetrasaccharide”. X-ray diffraction, 4 ligands (AMV, AMU, NAG), 4 pockets (best druggability 0.35). MolNFT v1 #87052 on GenesisL1: 3D structure…
- PDB
- 4BPA
- Type
- protein
- Length
- 482 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMPDH2
- UniProt
- Q9HT86
- Ligands
- AMV, AMU, NAG, ZN
- Pockets
- 4 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | AMPDH2 | protein | 241 | 37% helix, 17% strand | Q9HT86 |
Ligands and binding sites
- AMV · methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside · ligand · chains B
- AMU · N-acetyl-beta-muramic acid · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains 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
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.35 | 0.74 | 18 | ZN |
| 2 | 80 | 0.34 | 0.75 | 16 | AMU, NAG |
| 3 | 81 | 0.34 | 0.75 | 20 | AMV, ZN |
| 4 | 74 | 0.30 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2421 Ų buried · 65 hydrogen bonds · protein-protein
Compared structures
- 4BPA · Crystal structure of AmpDh2 from Pseudomonas aeruginosa in complex with NAG-NAM-NAG-NAM… · 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 4BPA · PDBe 4BPA · UniProt Q9HT86
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