MolNFT v1 · #51638 · protein
Crystal structure of the open state of tolc outer membrane component of mutlidrug efflux pumps
2VDD · Outer membrane protein tolc: “Crystal structure of the open state of tolc outer membrane component of mutlidrug efflux pumps”. X-ray diffraction, 2 ligands (K, CL), 20 pockets (best druggability 0.76). MolNFT v1 #51638 on GenesisL1…
- 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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