Research workbench
Structure of the siderophore periplasmic binding protein from the fuscachelin gene cluster of thermobifida fusca in P21
Analyse Structure of the siderophore periplasmic binding protein from the fuscachelin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DH1
- Type
- protein
- Length
- 1,103 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Siderophore periplasmic binding protein
- UniProt
- Q47NS2
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Siderophore periplasmic binding protein | protein | 277 | 47% helix, 19% strand | Q47NS2 |
| B | Siderophore periplasmic binding protein | protein | 276 | 49% helix, 20% strand | Q47NS2 |
| C | Siderophore periplasmic binding protein | protein | 274 | 47% helix, 19% strand | Q47NS2 |
| D | Siderophore periplasmic binding protein | protein | 276 | 46% helix, 19% strand | Q47NS2 |
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.73 | 0.76 | 88 | empty |
| 2 | 798 | 0.72 | 0.77 | 58 | empty |
| 3 | 390 | 0.58 | 0.75 | 43 | empty |
| 4 | 303 | 0.58 | 0.77 | 43 | empty |
| 5 | 305 | 0.57 | 0.76 | 42 | empty |
Interfaces
3 interfaces between chains.
- B–D · 629 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 620 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 94 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5DH1 · Structure of the siderophore periplasmic binding protein from the fuscachelin gene… · 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 Q47NS2
- Elsewhere: RCSB PDB 5DH1 · PDBe 5DH1 · UniProt Q47NS2
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