Research workbench
Cryoem structure of the RIX7 D2 walker B mutant
Analyse Cryoem structure of the RIX7 D2 walker B mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T3I
- Type
- protein
- Length
- 3,464 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RIX7; Substrate peptide
- UniProt
- G0RZG1
- Ligands
- ATP, PO4
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RIX7 | protein | 577 | 49% helix, 10% strand | G0RZG1 |
| B, C, D | RIX7 | protein | 578 | 51% helix, 10% strand | G0RZG1 |
| E | RIX7 | protein | 574 | 49% helix, 10% strand | G0RZG1 |
| F | RIX7 | protein | 552 | 53% helix, 9% strand | G0RZG1 |
| G | Substrate peptide | protein | 27 | 0% helix, 19% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D, E
- PO4 · Phosphate ion · ion · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.84 | 0.85 | 129 | empty |
| 2 | 1061 | 0.82 | 0.83 | 109 | ATP |
| 3 | 859 | 0.80 | 0.83 | 87 | ATP |
| 4 | 664 | 0.80 | 0.85 | 58 | ATP |
| 5 | 1081 | 0.80 | 0.81 | 101 | PO4 |
Interfaces
15 interfaces between chains.
- A–B · 4804 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 4654 Ų buried · 44 hydrogen bonds · protein-protein
- D–E · 4493 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 4418 Ų buried · 40 hydrogen bonds · protein-protein
- A–F · 2633 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7T3I · CryoEM structure of the Rix7 D2 Walker B mutant · 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 G0RZG1
- Elsewhere: RCSB PDB 7T3I · PDBe 7T3I · UniProt G0RZG1
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