MolNFT v1 · #51639 · protein
Crystal structure of the open state of tolc outer membrane component of mutlidrug efflux pumps
2VDE · Outer membrane protein tolc: “Crystal structure of the open state of tolc outer membrane component of mutlidrug efflux pumps”. X-ray diffraction, 1 ligand (CL), 15 pockets (best druggability 0.70). MolNFT v1 #51639 on GenesisL1: 3D…
- PDB
- 2VDE
- 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
- CL
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Outer membrane protein tolc | protein | 428 | 66% helix, 16% strand | P02930 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.70 | 0.76 | 97 | empty |
| 2 | 160 | 0.48 | 0.76 | 22 | empty |
| 3 | 158 | 0.47 | 0.76 | 25 | empty |
| 4 | 94 | 0.43 | 0.79 | 13 | empty |
| 5 | 73 | 0.37 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2532 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 2468 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 2428 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 2VDE · 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 0.98
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 2VDE · PDBe 2VDE · UniProt P02930
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