Research workbench
Paenibacillus sp. YM1 laminaribiose phosphorylase with alpha-glc-1- phosphate bound
Analyse Paenibacillus sp. YM1 laminaribiose phosphorylase with alpha-glc-1- phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GH2
- Type
- protein
- Length
- 1,813 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laminaribiose phosphorylase
- EC
- 2.4.1.31
- UniProt
- D7UT17
- Ligands
- G1P, CL, SO4
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laminaribiose phosphorylase (EC 2.4.1.31) | protein | 908 | 32% helix, 27% strand | D7UT17 |
| B | Laminaribiose phosphorylase (EC 2.4.1.31) | protein | 905 | 32% helix, 27% strand | D7UT17 |
Ligands and binding sites
- G1P · 1-O-phosphono-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.82 | 0.92 | 72 | CL |
| 2 | 165 | 0.81 | 0.97 | 35 | empty |
| 3 | 1129 | 0.80 | 0.81 | 89 | G1P, EDO, CL |
| 4 | 501 | 0.75 | 0.83 | 36 | empty |
| 5 | 622 | 0.74 | 0.81 | 46 | G1P, CL |
Interfaces
1 interface between chains.
- A–B · 3556 Ų buried · 58 hydrogen bonds · protein-protein
Compared structures
- 6GH2 · Paenibacillus sp. YM1 laminaribiose phosphorylase with alpha-glc-1-phosphate bound · 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 D7UT17
- Elsewhere: RCSB PDB 6GH2 · PDBe 6GH2 · UniProt D7UT17
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