Research workbench

Crystal structure determination of methemoglobin from pigeon at 2 ångström resolution (columba livia)

Analyse Crystal structure determination of methemoglobin from pigeon at 2 ångström… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DHR
Type: protein
Length: 1,144 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemoglobin subunit alpha-a; Hemoglobin subunit beta
UniProt: P21871, P11342
Ligands: HEM
Pockets: 13 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Hemoglobin subunit alpha-a	protein	141	74% helix, 0% strand	P21871
B, D, F, H	Hemoglobin subunit beta	protein	145	81% helix, 0% strand	P11342

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, H, D, E, F, G

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1191	0.87	0.88	121	empty
2	1069	0.87	0.88	131	empty
3	1044	0.81	0.82	100	HEM
4	256	0.76	0.89	31	HEM
5	269	0.75	0.88	31	HEM

Interfaces

16 interfaces between chains.

G–H · 915 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 906 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 904 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 902 Å² buried · 8 hydrogen bonds · protein-protein
F–G · 589 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3DHR · Crystal Structure Determination of Methemoglobin from Pigeon at 2 Angstrom Resolution… · the same entry in another collection · chain H against H, TM-score 1.00
P11342 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P11342) · a predicted model of the same protein · chain B against A, TM-score 0.99
P21871 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha-a (P21871) · a predicted model of the same protein · chain A 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 P21871
Every structure of UniProt P11342
Elsewhere: RCSB PDB 3DHR · PDBe 3DHR · UniProt P21871 · UniProt P11342

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