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Crosslinked ALPHA(NI)-BETA(NI) human hemoglobin a in the T quaternary structure at 95 K: light

Analyse Crosslinked ALPHA(NI)-BETA(NI) human hemoglobin a in the T quaternary structure… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LCX
Type: protein
Length: 1,148 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemoglobin subunit alpha; Hemoglobin subunit beta
UniProt: P69905, P68871
Ligands: HNI, 2FU
Pockets: 19 · best druggability 0.82

Structure

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

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

Ligands and binding sites

HNI · Protoporphyrin IX containing ni(ii) · ligand · 8 copies · chains A, B, C, D, E, F, G, H
2FU · But-2-enedial · ligand · 2 copies · chains B, D, F, H

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

Pockets

19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1021	0.82	0.83	100	empty
2	934	0.82	0.84	92	empty
3	828	0.74	0.78	59	HNI
4	236	0.74	0.88	29	HNI
5	231	0.74	0.88	30	HNI

Interfaces

13 interfaces between chains.

G–H · 848 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 846 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 842 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 836 Å² buried · 10 hydrogen bonds · protein-protein
E–H · 712 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

6LCX · Crosslinked alpha(Ni)-beta(Ni) human hemoglobin A in the T quaternary structure at 95 K… · 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 6LCX · PDBe 6LCX · UniProt P69905 · UniProt P68871

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