Research workbench
Crystal structure of peptide transporter dtpa-nanobody in mes buffer
Analyse Crystal structure of peptide transporter dtpa-nanobody in mes buffer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GS1
- Type
- protein
- Length
- 597 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptide and tripeptide permease a; Nanobody 00
- UniProt
- P77304
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptide and tripeptide permease a | protein | 472 | 80% helix, 1% strand | P77304 |
| H | Nanobody 00 | protein | 125 | 2% helix, 46% strand | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.79 | 0.80 | 72 | empty |
| 2 | 117 | 0.51 | 0.81 | 23 | empty |
| 3 | 145 | 0.48 | 0.77 | 20 | empty |
| 4 | 105 | 0.42 | 0.78 | 17 | empty |
| 5 | 55 | 0.35 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–H · 915 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6GS1 · Crystal structure of peptide transporter DtpA-nanobody in MES buffer · the same entry in another collection · chain A against A, TM-score 1.00
- P77304 · AlphaFold monomer V2.0 prediction for dipeptide and tripeptide permease a (P77304) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P77304
- Elsewhere: RCSB PDB 6GS1 · PDBe 6GS1 · UniProt P77304
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