Research workbench
The crystal structure of the outer-membrane transporter yncd
Analyse The crystal structure of the outer-membrane transporter yncd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V81
- Type
- protein
- Length
- 652 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable tonb-dependent receptor yncd
- UniProt
- P76115
- Ligands
- CA
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable tonb-dependent receptor yncd | protein | 652 | 5% helix, 57% strand | P76115 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.85 | 0.94 | 51 | empty |
| 2 | 1090 | 0.81 | 0.82 | 85 | empty |
| 3 | 516 | 0.75 | 0.84 | 55 | empty |
| 4 | 756 | 0.73 | 0.78 | 76 | empty |
| 5 | 267 | 0.59 | 0.79 | 31 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6V81 · The crystal structure of the outer-membrane transporter YncD · the same entry in another collection · chain A against A, TM-score 1.00
- P76115 · AlphaFold monomer V2.0 prediction for probable tonb-dependent receptor yncd (P76115) · 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 P76115
- Elsewhere: RCSB PDB 6V81 · PDBe 6V81 · UniProt P76115
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