Research workbench
Guanylylpyridinol (gp)- and ATP-bound hcge from methanothermobacter marburgensis
Analyse Guanylylpyridinol (gp)- and ATP-bound hcge from methanothermobacter marburgensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WV9
- Type
- protein
- Length
- 820 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hmd co-occurring protein hcge
- EC
- 2.7.7.-
- UniProt
- D9PY12
- Ligands
- ATP, FEG, SO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Hmd co-occurring protein hcge (EC 2.7.7.-) | protein | 205 | 36% helix, 19% strand | D9PY12 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- FEG · 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.69 | 0.82 | 44 | ATP, FEG |
| 2 | 484 | 0.68 | 0.79 | 73 | empty |
| 3 | 338 | 0.66 | 0.80 | 43 | ATP, FEG |
| 4 | 363 | 0.65 | 0.79 | 41 | ATP, FEG |
| 5 | 220 | 0.64 | 0.83 | 35 | empty |
Interfaces
3 interfaces between chains.
- B–D · 771 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 751 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3WV9 · Guanylylpyridinol (GP)- and ATP-bound HcgE from Methanothermobacter marburgensis · 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 D9PY12
- Elsewhere: RCSB PDB 3WV9 · PDBe 3WV9 · UniProt D9PY12
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.