MolNFT v1 · #116544 · protein
Structure of the siderophore periplasmic binding protein from the fuscachelin gene cluster of thermobifida fusca in P21
5DH1: “Structure of the siderophore periplasmic binding protein from the fuscachelin gene cluster of thermobifida…”. X-ray diffraction, 6 pockets (best druggability 0.73). MolNFT v1 #116544 on GenesisL1: 3D structure, binding sites and…
- 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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