MolNFT v1 · #188320 · protein
Crystal structure of alpha-1,4 glucan phosphorylase from klebsiella pneumoniae
7TM7: “Crystal structure of alpha-1,4 glucan phosphorylase from klebsiella pneumoniae”. X-ray diffraction, 1 ligand (PLP), 19 pockets (best druggability 0.86). MolNFT v1 #188320 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7TM7
- Type
- protein
- Length
- 1,593 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,4 glucan phosphorylase
- EC
- 2.4.1.1
- UniProt
- A0A0H3GYH4
- Ligands
- PLP
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,4 glucan phosphorylase (EC 2.4.1.1) | protein | 802 | 53% helix, 13% strand | A0A0H3GYH4 |
| B | Alpha-1,4 glucan phosphorylase (EC 2.4.1.1) | protein | 791 | 54% helix, 14% strand | A0A0H3GYH4 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.86 | 0.88 | 106 | empty |
| 2 | 1001 | 0.80 | 0.81 | 92 | PLP |
| 3 | 1085 | 0.79 | 0.81 | 98 | PLP |
| 4 | 53 | 0.73 | 0.99 | 16 | empty |
| 5 | 52 | 0.72 | 0.99 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2130 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7TM7 · Crystal structure of Alpha-1,4 glucan phosphorylase from Klebsiella pneumoniae · 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 A0A0H3GYH4
- Elsewhere: RCSB PDB 7TM7 · PDBe 7TM7 · UniProt A0A0H3GYH4
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