Research workbench
Crystal structure of iron uptake ABC transporter substrate-binding protein piaa from streptococcus pneumoniae canada MDR_19A bound to hydroxymate siderophore ferrioxamine E and IRON(III)
Analyse Crystal structure of iron uptake ABC transporter substrate-binding protein piaa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JJ5
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter substrate-binding protein-iron transport
- UniProt
- A0A062WLD9
- Ligands
- 6L0, FE, CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter substrate-binding protein-iron transport | protein | 308 | 41% helix, 17% strand | A0A062WLD9 |
| B | ABC transporter substrate-binding protein-iron transport | protein | 304 | 41% helix, 17% strand | A0A062WLD9 |
Ligands and binding sites
- 6L0 · (8E)-6,17,28-trihydroxy-1,6,12,17,23,28-hexaazacyclotritriacont-8-ene-2,5,13,16,24,27-hexone · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.76 | 0.80 | 75 | FE, 6L0 |
| 2 | 429 | 0.64 | 0.78 | 53 | FE, 6L0 |
| 3 | 57 | 0.28 | 0.74 | 13 | empty |
| 4 | 51 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 596 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5JJ5 · Crystal structure of iron uptake ABC transporter substrate-binding protein PiaA from… · 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 A0A062WLD9
- Elsewhere: RCSB PDB 5JJ5 · PDBe 5JJ5 · UniProt A0A062WLD9
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