Research workbench
Atomic structure of a novel tryptophan-zipper pentamer
Analyse Atomic structure of a novel tryptophan-zipper pentamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T8Z
- Type
- protein
- Length
- 247 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major outer membrane lipoprotein
- UniProt
- P69776
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 94% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Major outer membrane lipoprotein | protein | 50 | 96% helix, 0% strand | P69776 |
| C | Major outer membrane lipoprotein | protein | 51 | 96% helix, 0% strand | P69776 |
| D | Major outer membrane lipoprotein | protein | 47 | 94% helix, 0% strand | P69776 |
| E | Major outer membrane lipoprotein | protein | 49 | 92% helix, 0% strand | P69776 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, C, A, D, E
- 12P · Dodecaethylene glycol · additive · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.89 | 0.90 | 87 | SO4, 12P |
Interfaces
6 interfaces between chains.
- C–D · 1182 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1166 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 1161 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1148 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1060 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1T8Z · Atomic Structure of A Novel Tryptophan-Zipper Pentamer · the same entry in another collection · chain E against E, TM-score 1.00
- P69776 · AlphaFold monomer V2.0 prediction for major outer membrane lipoprotein lpp (P69776) · a predicted model of the same protein · chain C against A, TM-score 0.90
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 P69776
- Elsewhere: RCSB PDB 1T8Z · PDBe 1T8Z · UniProt P69776
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