MolNFT v1 · #150011 · protein
Paenibacillus sp. YM1 laminaribiose phosphorylase with alpha-man-1- phosphate bound
6GH3: “Paenibacillus sp. YM1 laminaribiose phosphorylase with alpha-man-1- phosphate bound”. X-ray diffraction, 3 ligands (M1P, CL, SO4), 15 pockets (best druggability 0.83). MolNFT v1 #150011 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6GH3
- Type
- protein
- Length
- 1,801 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
- M1P, CL, SO4
- Pockets
- 15 · best druggability 0.83
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 | 902 | 32% helix, 27% strand | D7UT17 |
| B | Laminaribiose phosphorylase (EC 2.4.1.31) | protein | 899 | 32% helix, 27% strand | D7UT17 |
Ligands and binding sites
- M1P · 1-O-phosphono-alpha-D-mannopyranose · 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 · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.83 | 0.96 | 45 | EDO |
| 2 | 1096 | 0.82 | 0.84 | 95 | M1P, CL |
| 3 | 1072 | 0.80 | 0.81 | 84 | M1P, EDO, CL |
| 4 | 131 | 0.79 | 0.97 | 29 | empty |
| 5 | 323 | 0.71 | 0.84 | 60 | CL |
Interfaces
1 interface between chains.
- A–B · 3555 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 6GH3 · Paenibacillus sp. YM1 laminaribiose phosphorylase with alpha-man-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 6GH3 · PDBe 6GH3 · UniProt D7UT17
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