MolNFT v1 · #21285 · protein
Crystal structure of "truncated" hemoglobin N (hbn) from mycobacterium tuberculosis, soaked with xe atoms
1S56 · Hemoglobin-like protein hbn: “Crystal structure of "truncated" hemoglobin N (hbn) from mycobacterium tuberculosis, soaked with xe atoms”. X-ray diffraction, 6 ligands (HEC, HEM, K), 3 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 1S56
- Type
- protein
- Length
- 263 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin-like protein hbn
- UniProt
- P0A592
- Ligands
- HEC, HEM, K, XE, CYN, PO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin-like protein hbn | protein | 128 | 68% helix, 0% strand | P0A592 |
| B | Hemoglobin-like protein hbn | protein | 135 | 64% helix, 1% strand | P0A592 |
Ligands and binding sites
- HEC · Heme C · ligand · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · chains B
- K · Potassium ion · metal · chains A
- XE · Xenon · ion · 8 copies · chains A, B
- CYN · Cyanide ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.78 | 0.88 | 31 | CYN, HEC, XE |
| 2 | 385 | 0.74 | 0.84 | 40 | CYN, HEM, XE |
| 3 | 54 | 0.25 | 0.72 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 234 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1S56 · Crystal Structure of Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis · 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 P0A592
- Elsewhere: RCSB PDB 1S56 · PDBe 1S56 · UniProt P0A592
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