Research workbench
Crystal structure of the truncated hemoglobin from geobacillus stearothermophilus
Analyse Crystal structure of the truncated hemoglobin from geobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BKM
- Type
- protein
- Length
- 256 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Truncated hemoglobin from geobacillus stearothermophilus
- UniProt
- Q5L1S0
- Ligands
- HEM, OXY
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Truncated hemoglobin from geobacillus stearothermophilus | protein | 128 | 66% helix, 0% strand | Q5L1S0 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · 2 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
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.76 | 0.87 | 28 | OXY, HEM, ACT |
| 2 | 299 | 0.73 | 0.86 | 27 | OXY, HEM, ACT |
| 3 | 331 | 0.56 | 0.75 | 39 | empty |
| 4 | 309 | 0.55 | 0.75 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 852 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2BKM · Crystal structure of the truncated hemoglobin from Geobacillus stearothermophilus · 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 Q5L1S0
- Elsewhere: RCSB PDB 2BKM · PDBe 2BKM · UniProt Q5L1S0
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