Research workbench
Crystal structure of mycobacterium tuberculosis trhbn TYRB10PHE mutant
Analyse Crystal structure of mycobacterium tuberculosis trhbn TYRB10PHE mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GKM
- Type
- protein
- Length
- 253 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin-like protein hbn
- UniProt
- P0A592
- Ligands
- HEM, NA, CYN
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin-like protein hbn | protein | 127 | 69% helix, 0% strand | P0A592 |
| B | Hemoglobin-like protein hbn | protein | 126 | 67% helix, 0% strand | P0A592 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- CYN · Cyanide ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.77 | 0.88 | 30 | CYN, HEM |
| 2 | 361 | 0.74 | 0.85 | 39 | CYN, HEM |
| 3 | 67 | 0.28 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 255 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2GKM · Crystal structure of Mycobacterium tuberculosis trHbN TyrB10Phe mutant · 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 2GKM · PDBe 2GKM · UniProt P0A592
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