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Capturing the haemoglobin allosteric transition in a single crystal form; crystal structure of half-liganded human haemoglobin with phosphate at 2.5 a resolution.

Analyse Capturing the haemoglobin allosteric transition in a single crystal form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4N7O
Type: protein
Length: 1,722 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemoglobin subunit alpha; Hemoglobin subunit beta
UniProt: P69905, P68871
Ligands: HNI, HEM
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K	Hemoglobin subunit alpha	protein	141	76% helix, 0% strand	P69905
B, D, F, H, J, L	Hemoglobin subunit beta	protein	146	77% helix, 0% strand	P68871

Ligands and binding sites

HNI · Protoporphyrin IX containing ni(ii) · ligand · 6 copies · chains A, D, E, H, I, L
HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains B, C, F, G, J, K

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	709	0.84	0.87	76	empty
2	621	0.82	0.87	68	empty
3	446	0.82	0.89	48	empty
4	915	0.81	0.83	79	empty
5	695	0.81	0.85	72	empty

Interfaces

24 interfaces between chains.

C–D · 953 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 943 Å² buried · 9 hydrogen bonds · protein-protein
G–H · 925 Å² buried · 11 hydrogen bonds · protein-protein
I–J · 919 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 909 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4N7O · Capturing the haemoglobin allosteric transition in a single crystal form; Crystal… · 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 P69905
Every structure of UniProt P68871
Elsewhere: RCSB PDB 4N7O · PDBe 4N7O · UniProt P69905 · UniProt P68871

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