MolNFT v1 · #168994 · protein
Colicin E1 fragment in nanodisc-embedded tolc
6WXH · Outer membrane protein tolc: “Colicin E1 fragment in nanodisc-embedded tolc”. Electron microscopy, 16 pockets (best druggability 0.82). MolNFT v1 #168994 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WXH
- Type
- protein
- Length
- 1,370 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein tolc; Colicin-E1
- UniProt
- P02930, P02978
- Pockets
- 16 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 73% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Outer membrane protein tolc | protein | 428 | 69% helix, 17% strand | P02930 |
| D | Colicin-E1 | protein | 86 | 91% helix, 0% strand | P02978 |
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.82 | 0.83 | 119 | empty |
| 2 | 1033 | 0.81 | 0.82 | 109 | empty |
| 3 | 631 | 0.75 | 0.82 | 102 | empty |
| 4 | 347 | 0.58 | 0.76 | 45 | empty |
| 5 | 152 | 0.56 | 0.82 | 25 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2511 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 2490 Ų buried · 56 hydrogen bonds · protein-protein
- A–C · 2469 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 2458 Ų buried · 50 hydrogen bonds · protein-protein
- A–D · 696 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6WXH · Colicin E1 fragment in nanodisc-embedded TolC · 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
- P02978 · AlphaFold monomer V2.0 prediction for colicin-E1 (P02978) · a predicted model of the same protein · chain D 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 P02930
- Every structure of UniProt P02978
- Elsewhere: RCSB PDB 6WXH · PDBe 6WXH · UniProt P02930 · UniProt P02978
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