MolNFT v1 · #150006 · protein
Paenibacillus sp. YM1 laminaribiose phosphorylase with sulphate bound
6GGY: “Paenibacillus sp. YM1 laminaribiose phosphorylase with sulphate bound”. X-ray diffraction, 2 ligands (SO4, CL), 20 pockets (best druggability 0.84). MolNFT v1 #150006 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GGY
- 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
- SO4, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laminaribiose phosphorylase (EC 2.4.1.31) | protein | 908 | 32% helix, 26% strand | D7UT17 |
| B | Laminaribiose phosphorylase (EC 2.4.1.31) | protein | 905 | 32% helix, 27% strand | D7UT17 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.84 | 0.97 | 49 | EDO |
| 2 | 948 | 0.81 | 0.82 | 85 | SO4, EDO, CL |
| 3 | 137 | 0.80 | 0.98 | 36 | empty |
| 4 | 130 | 0.79 | 0.97 | 29 | empty |
| 5 | 633 | 0.75 | 0.81 | 60 | SO4, CL |
Interfaces
1 interface between chains.
- A–B · 3546 Ų buried · 65 hydrogen bonds · protein-protein
Compared structures
- 6GGY · Paenibacillus sp. YM1 laminaribiose phosphorylase with sulphate 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 6GGY · PDBe 6GGY · UniProt D7UT17
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