Research workbench
MSP1-substrate complex in closed conformation
Analyse MSP1-substrate complex in closed conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PDW
- Type
- protein
- Length
- 1,460 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane-spanning ATPase-like protein; Unknown peptide
- UniProt
- G0S654
- Ligands
- ADP, BEF, MG
- Pockets
- 18 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 45% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Membrane-spanning ATPase-like protein | protein | 294 | 45% helix, 7% strand | G0S654 |
| C | Membrane-spanning ATPase-like protein | protein | 298 | 50% helix, 9% strand | G0S654 |
| D | Membrane-spanning ATPase-like protein | protein | 299 | 48% helix, 9% strand | G0S654 |
| E | Membrane-spanning ATPase-like protein | protein | 298 | 42% helix, 10% strand | G0S654 |
| F | Membrane-spanning ATPase-like protein | protein | 261 | 40% helix, 8% strand | G0S654 |
| G | Unknown peptide | protein | 10 | 0% helix, 20% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains B, C, D, E, F
- BEF · Beryllium trifluoride ion · ligand · 3 copies · chains B, C, D, E
- MG · Magnesium ion · metal · 4 copies · chains B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.82 | 0.86 | 80 | ADP, BEF, MG |
| 2 | 728 | 0.81 | 0.85 | 93 | ADP, MG |
| 3 | 1191 | 0.81 | 0.83 | 100 | ADP, BEF |
| 4 | 671 | 0.81 | 0.86 | 75 | ADP, MG, BEF |
| 5 | 691 | 0.73 | 0.80 | 57 | empty |
Interfaces
10 interfaces between chains.
- D–E · 2297 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2241 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 2188 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1928 Ų buried · 11 hydrogen bonds · protein-protein
- C–G · 224 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6PDW · Msp1-substrate complex in closed conformation · the same entry in another collection · chain B against B, 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 G0S654
- Elsewhere: RCSB PDB 6PDW · PDBe 6PDW · UniProt G0S654
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.