MolNFT v1 · #34122 · protein
The crystal structure of oligopeptide binding protein from thermus thermophilus HB8 complexed with pentapeptide
2D5W · Peptide ABC transporter, peptide-binding protein: “The crystal structure of oligopeptide binding protein from thermus thermophilus HB8 complexed with…”. X-ray diffraction, 9 pockets (best druggability 0.87). MolNFT v1 #34122 on…
- 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
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