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Crystallographic structure of mycobacterium tuberculosis hemoglobin O

Analyse Crystallographic structure of mycobacterium tuberculosis hemoglobin O in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NGK
Type: protein
Length: 1,520 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemoglobin-like protein hbo
UniProt: P0A595
Ligands: HEM, SO4, CYN
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 66% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, F	Hemoglobin-like protein hbo	protein	126	67% helix, 0% strand	P0A595
B, E, G, H, I, J, K, L	Hemoglobin-like protein hbo	protein	127	65% helix, 0% strand	P0A595

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, H, B, I, C, G, D, K, E, L, F, J
SO4 · Sulfate ion · ion · 18 copies · chains A, H, G, L, B, I, E, J, C, D, K, F
CYN · Cyanide ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	462	0.83	0.89	45	CYN, HEM, SO4
2	431	0.82	0.90	48	SO4, CYN, HEM
3	458	0.82	0.89	49	SO4, CYN, HEM
4	444	0.82	0.89	48	SO4, CYN, HEM
5	464	0.82	0.89	49	SO4, CYN, HEM

Interfaces

33 interfaces between chains.

B–H · 730 Å² buried · 4 hydrogen bonds · protein-protein
A–G · 712 Å² buried · 7 hydrogen bonds · protein-protein
C–I · 704 Å² buried · 5 hydrogen bonds · protein-protein
E–J · 701 Å² buried · 5 hydrogen bonds · protein-protein
F–K · 669 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1NGK · Crystallographic Structure of Mycobacterium tuberculosis Hemoglobin O · 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 P0A595
Elsewhere: RCSB PDB 1NGK · PDBe 1NGK · UniProt P0A595

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