MolNFT v1 · #139036 · protein

Direct observation of conformational population shifts in hemoglobin: crystal structure of half-liganded hemoglobin after adding 4 mm bezafibrate pH 6.5.

5X2S · Hemoglobin subunit alpha: “Direct observation of conformational population shifts in hemoglobin: crystal structure of half-liganded…”. X-ray diffraction, 3 ligands (HNI, HEM, PEM), 20 pockets (best druggability 0.86). MolNFT v1…

PDB: 5X2S
Type: protein
Length: 1,710 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, PEM
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K	Hemoglobin subunit alpha	protein	140	72% helix, 0% strand	P69905
B, D, F, H, J, L	Hemoglobin subunit beta	protein	145	79% 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
PEM · 2-[P-[2-P-chlorobenzamido)ethyl]phenoxy]-2-methylpropionic acid · ligand · chains 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	1171	0.86	0.87	101	empty
2	894	0.83	0.85	74	empty
3	881	0.83	0.85	57	empty
4	126	0.79	0.96	21	empty
5	100	0.77	0.97	18	empty

Interfaces

25 interfaces between chains.

E–F · 959 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 957 Å² buried · 11 hydrogen bonds · protein-protein
G–H · 954 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 929 Å² buried · 10 hydrogen bonds · protein-protein
I–J · 921 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5X2S · Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure… · the same entry in another collection · chain I against I, 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 5X2S · PDBe 5X2S · UniProt P69905 · UniProt P68871

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