Research workbench
Periplasmic heme-binding protein bhut in complex with one heme (holo- 1)
Analyse Periplasmic heme-binding protein bhut in complex with one heme (holo- 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y89
- Type
- protein
- Length
- 534 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative hemin transport system, substrate-binding protein
- UniProt
- B4EKB3
- Ligands
- HEM, SO4
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative hemin transport system, substrate-binding protein | protein | 267 | 45% helix, 18% strand | B4EKB3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.65 | 0.82 | 41 | HEM, ACT |
| 2 | 267 | 0.65 | 0.82 | 38 | HEM, ACT |
| 3 | 228 | 0.63 | 0.82 | 29 | SO4 |
Interfaces
1 interface between chains.
- A–B · 427 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5Y89 · Periplasmic heme-binding protein BhuT in complex with one heme (holo-1) · the same entry in another collection · chain B against B, 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 B4EKB3
- Elsewhere: RCSB PDB 5Y89 · PDBe 5Y89 · UniProt B4EKB3
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