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Crystal structure determination of goat hemoglobin (capra hircus) at 3 ångström resolution

Analyse Crystal structure determination of goat hemoglobin (capra hircus) at 3 ångström… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EU1
Type: protein
Length: 572 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemoglobin subunit alpha-1/2; Hemoglobin subunit beta-a
UniProt: P68238, P02077
Ligands: HEM
Pockets: 6 · best druggability 0.87

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Hemoglobin subunit alpha-1/2	protein	141	73% helix, 0% strand	P68238
B, D	Hemoglobin subunit beta-a	protein	145	78% helix, 0% strand	P02077

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D

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

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	868	0.87	0.89	95	empty
2	252	0.76	0.88	34	HEM
3	254	0.75	0.88	28	HEM
4	254	0.75	0.87	30	HEM
5	180	0.72	0.88	24	HEM

Interfaces

6 interfaces between chains.

C–D · 897 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 854 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 551 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 530 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 257 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3EU1 · Crystal Structure determination of goat hemoglobin (Capra hircus) at 3 angstrom resolution · the same entry in another collection · chain A against A, TM-score 1.00
P02077 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta-a (P02077) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P68238
Every structure of UniProt P02077
Elsewhere: RCSB PDB 3EU1 · PDBe 3EU1 · UniProt P68238 · UniProt P02077

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