Research workbench
Structure of E. COLI letb delta (RING6) mutant, RING1 in the closed state (model 1)
Analyse Structure of E. COLI letb delta (RING6) mutant, RING1 in the closed state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SEE
- Type
- protein
- Length
- 4,314 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mce family protein, intermembrane transport protein yebt chimera
- UniProt
- A0A769F599, P76272
- Ligands
- UNX
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Mce family protein, intermembrane transport protein yebt chimera | protein | 719 | 11% helix, 38% strand | A0A769F599, P76272 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 6 copies · chains A, B, C, D, E, F
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 | 939 | 0.80 | 0.82 | 131 | empty |
| 2 | 868 | 0.79 | 0.82 | 123 | empty |
| 3 | 987 | 0.73 | 0.77 | 110 | empty |
| 4 | 386 | 0.72 | 0.83 | 53 | empty |
| 5 | 300 | 0.71 | 0.84 | 57 | empty |
Interfaces
6 interfaces between chains.
- E–F · 4405 Ų buried · 41 hydrogen bonds · protein-protein
- A–F · 4306 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 4195 Ų buried · 33 hydrogen bonds · protein-protein
- D–E · 4193 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 4099 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 7SEE · Structure of E. coli LetB delta (Ring6) mutant, Ring1 in the closed state (Model 1) · the same entry in another collection · chain A against A, TM-score 1.00
- P76272 · AlphaFold monomer V2.0 prediction for intermembrane transport protein yebt (P76272) · a predicted model of the same protein · chain A against A, TM-score 0.80
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 A0A769F599
- Every structure of UniProt P76272
- Elsewhere: RCSB PDB 7SEE · PDBe 7SEE · UniProt A0A769F599 · UniProt P76272
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