Research workbench
Crystal structure of the open state of tolc outer membrane component of mutlidrug efflux pumps
Analyse Crystal structure of the open state of tolc outer membrane component of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VDD
- Type
- protein
- Length
- 1,284 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein tolc
- UniProt
- P02930
- Ligands
- K, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 63% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Outer membrane protein tolc | protein | 428 | 63% helix, 16% strand | P02930 |
Ligands and binding sites
- K · Potassium ion · metal · 3 copies · chains A, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.76 | 0.78 | 113 | empty |
| 2 | 75 | 0.54 | 0.86 | 18 | empty |
| 3 | 128 | 0.46 | 0.77 | 21 | empty |
| 4 | 102 | 0.41 | 0.76 | 17 | empty |
| 5 | 76 | 0.41 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2559 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 2534 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 2504 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 2VDD · Crystal Structure of the Open State of TolC Outer Membrane Component of Mutlidrug Efflux… · the same entry in another collection · chain A against A, TM-score 1.00
- P02930 · AlphaFold monomer V2.0 prediction for outer membrane protein tolc (P02930) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P02930
- Elsewhere: RCSB PDB 2VDD · PDBe 2VDD · UniProt P02930
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