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Structure of human foetal deoxyhaemoglobin

Analyse Structure of human foetal deoxyhaemoglobin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1FDH
Type: protein
Length: 574 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemoglobin F (deoxy) (alpha chain); Hemoglobin F (deoxy) (gamma chain)
UniProt: P69905, P69891
Ligands: HEM, ACE
Pockets: 9 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Hemoglobin F (deoxy) (alpha chain)	protein	141	72% helix, 0% strand	P69905
G, H	Hemoglobin F (deoxy) (gamma chain)	protein	146	75% helix, 0% strand	P69891

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, G, B, H
ACE · Acetyl group · ligand · 2 copies · chains G, H

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

Pockets

9 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	790	0.80	0.83	79	empty
2	227	0.75	0.89	31	HEM
3	260	0.74	0.87	29	HEM
4	206	0.73	0.88	28	HEM
5	278	0.73	0.85	29	HEM

Interfaces

5 interfaces between chains.

A–G · 845 Å² buried · 6 hydrogen bonds · protein-protein
B–H · 845 Å² buried · 6 hydrogen bonds · protein-protein
A–H · 720 Å² buried · 6 hydrogen bonds · protein-protein
G–B · 720 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 312 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1FDH · Structure of human foetal deoxyhaemoglobin · the same entry in another collection · chain G against G, TM-score 1.00
P69891 · AlphaFold monomer V2.0 prediction for hemoglobin subunit gamma-1 (P69891) · a predicted model of the same protein · chain G 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 P69905
Every structure of UniProt P69891
Elsewhere: RCSB PDB 1FDH · PDBe 1FDH · UniProt P69905 · UniProt P69891

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