Research workbench
The crystal structure of oligopeptide binding protein from thermus thermophilus HB8 complexed with pentapeptide
Analyse The crystal structure of oligopeptide binding protein from thermus thermophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D5W
- Type
- protein
- Length
- 1,214 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide ABC transporter, peptide-binding protein; Pentapeptide a; Pentapeptide B
- UniProt
- Q5SHU6
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptide ABC transporter, peptide-binding protein | protein | 602 | 32% helix, 22% strand | Q5SHU6 |
| C | Pentapeptide a | protein | 5 | 0% helix, 40% strand | — |
| D | Pentapeptide B | protein | 5 | 0% helix, 40% strand | — |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.87 | 0.93 | 69 | empty |
| 2 | 458 | 0.86 | 0.93 | 68 | empty |
| 3 | 201 | 0.72 | 0.89 | 39 | empty |
| 4 | 65 | 0.46 | 0.83 | 16 | empty |
| 5 | 218 | 0.45 | 0.73 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 978 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 621 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 613 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2D5W · The crystal structure of oligopeptide binding protein from Thermus thermophilus HB8… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5SHU6
- Elsewhere: RCSB PDB 2D5W · PDBe 2D5W · UniProt Q5SHU6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.