MolNFT v1 · #111549 · protein

The crystal structure of mongoose (helogale parvula) hemoglobin at pH 8.2

4YU3: “The crystal structure of mongoose (helogale parvula) hemoglobin at pH 8.2”. X-ray diffraction, 2 ligands (HEM, OXY), 4 pockets (best druggability 0.74). MolNFT v1 #111549 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4YU3
Type: protein
Length: 287 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemoglobin
Ligands: HEM, OXY
Pockets: 4 · best druggability 0.74

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hemoglobin	protein	141	76% helix, 0% strand	—
B	Hemoglobin	protein	146	75% helix, 0% strand	—

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
OXY · Oxygen molecule · ion · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	248	0.74	0.88	29	HEM, OXY
2	200	0.70	0.86	24	HEM, OXY
3	123	0.54	0.82	25	empty
4	58	0.28	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 911 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4YU3 · The crystal structure of mongoose (Helogale parvula) hemoglobin at pH 8.2 · 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
Elsewhere: RCSB PDB 4YU3 · PDBe 4YU3

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