MolNFT v1 · #148878 · protein
Structure of ibps from dickeya dadantii
6FJL · ABC-type FE3+ transport system, periplasmic component: “Structure of ibps from dickeya dadantii”. X-ray diffraction, 1 ligand (MG), 14 pockets (best druggability 0.77). MolNFT v1 #148878 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6FJL
- 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
- MG
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ABC-type FE3+ transport system, periplasmic component | protein | 345 | 41% helix, 18% strand | E0SCP7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.77 | 0.84 | 79 | empty |
| 2 | 459 | 0.75 | 0.84 | 74 | empty |
| 3 | 249 | 0.74 | 0.88 | 51 | ACT |
| 4 | 310 | 0.72 | 0.85 | 55 | empty |
| 5 | 256 | 0.71 | 0.86 | 46 | ACT |
Interfaces
5 interfaces between chains.
- B–C · 472 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 467 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 453 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 380 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 78 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6FJL · Structure of IbpS from Dickeya dadantii · the same entry in another collection · chain D against D, 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 6FJL · PDBe 6FJL · UniProt E0SCP7
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