MolNFT v1 · #109362 · protein

Human haptoglobin-haemoglobin complex

4X0L · Hemoglobin subunit alpha: “Human haptoglobin-haemoglobin complex”. X-ray diffraction, 5 ligands (HEM, NAG, FUC), 11 pockets (best druggability 0.74). MolNFT v1 #109362 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4X0L
Type: protein
Length: 544 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemoglobin subunit alpha; Hemoglobin subunit beta; Haptoglobin
UniProt: P69905, P68871, P00738
Ligands: HEM, NAG, FUC, OXY, SO4
Pockets: 11 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hemoglobin subunit alpha	protein	141	77% helix, 0% strand	P69905
B	Hemoglobin subunit beta	protein	144	76% helix, 0% strand	P68871
C	Haptoglobin	protein	259	14% helix, 31% strand	P00738

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
FUC · alpha-L-fucopyranose · sugar
OXY · Oxygen molecule · ion · 2 copies · chains A, B
SO4 · Sulfate ion · ion · chains B, C
GOL · Glycerol · additive · 2 copies · chains B, C
CAC · Cacodylate ion · additive · chains C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	206	0.74	0.90	49	empty
2	227	0.72	0.87	26	HEM, OXY
3	192	0.69	0.86	24	HEM, OXY
4	158	0.64	0.85	30	empty
5	253	0.63	0.81	34	empty

Interfaces

3 interfaces between chains.

A–B · 848 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 812 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 812 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

4X0L · Human haptoglobin-haemoglobin complex · the same entry in another collection · chain C against C, TM-score 1.00
P00738 · AlphaFold monomer V2.0 prediction for haptoglobin (P00738) · a predicted model of the same protein · chain C against A, TM-score 0.96

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
Every structure of UniProt P00738
Elsewhere: RCSB PDB 4X0L · PDBe 4X0L · UniProt P69905 · UniProt P68871 · UniProt P00738

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