MolNFT v1 · #151228 · protein
Structure of iron bound ibps from dickeya dadantii
6HHB · ABC-type FE3+ transport system, periplasmic component: “Structure of iron bound ibps from dickeya dadantii”. X-ray diffraction, 1 ligand (FE), 9 pockets (best druggability 0.87). MolNFT v1 #151228 on GenesisL1: 3D structure, binding…
- PDB
- 6HHB
- Type
- protein
- Length
- 1,380 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC-type FE3+ transport system, periplasmic component
- UniProt
- E0SCP7
- Ligands
- FE
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ABC-type FE3+ transport system, periplasmic component | protein | 345 | 40% helix, 18% strand | E0SCP7 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.87 | 0.88 | 131 | FE |
| 2 | 1058 | 0.87 | 0.88 | 121 | FE |
| 3 | 131 | 0.45 | 0.77 | 18 | empty |
| 4 | 57 | 0.37 | 0.80 | 18 | empty |
| 5 | 67 | 0.34 | 0.77 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1305 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1286 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 297 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6HHB · Structure of iron bound IbpS from Dickeya dadantii · 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 E0SCP7
- Elsewhere: RCSB PDB 6HHB · PDBe 6HHB · UniProt E0SCP7
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