MolNFT v1 · #108828 · protein

Structure of T. brucei haptoglobin-hemoglobin receptor binding to human haptoglobin-hemoglobin

4WJG · Hemoglobin subunit alpha: “Structure of T. brucei haptoglobin-hemoglobin receptor binding to human haptoglobin-hemoglobin”. X-ray diffraction, 3 ligands (HEM, NAG, OXY), 20 pockets (best druggability 0.83). MolNFT v1 #108828 on…

PDB: 4WJG
Type: protein
Length: 6,012 residues
Chains: 30
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemoglobin subunit alpha; Hemoglobin subunit beta; Haptoglobin; Iron-regulated surface…
UniProt: P69905, P68871, P00738, Q99TD3, I7BA80
Ligands: HEM, NAG, OXY
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 47% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F, K, P, U, Z	Hemoglobin subunit alpha	protein	141	77% helix, 0% strand	P69905
B, G, L, Q, V, 1	Hemoglobin subunit beta	protein	146	80% helix, 0% strand	P68871
C, H, M, R, W, 2	Haptoglobin	protein	310	9% helix, 34% strand	P00738
D, I, N, S, X, 3	Iron-regulated surface determinant protein H	protein	144	11% helix, 44% strand	Q99TD3
E, J, O, T, Y, 4	Haptoglobin-hemoglobin receptor	protein	261	77% helix, 0% strand	I7BA80

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, B, E, F, G, J, K, L, O, P, Q, T, U, V, Y, Z, 1, 4
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 43 copies · chains C, H, M, R, E, W, 2, J, O, T, Y, 4
OXY · Oxygen molecule · ion · 12 copies · chains A, B, F, G, K, L, P, Q, U, V, Z, 1

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	696	0.83	0.86	70	HEM, OXY
2	1150	0.82	0.83	110	HEM, OXY
3	610	0.81	0.86	62	HEM, OXY
4	659	0.81	0.86	67	HEM, OXY
5	757	0.81	0.85	70	HEM, OXY

Interfaces

56 interfaces between chains.

W–2 · 1545 Å² buried · 27 hydrogen bonds · protein-protein
C–H · 1544 Å² buried · 27 hydrogen bonds · protein-protein
M–R · 1543 Å² buried · 27 hydrogen bonds · protein-protein
Z–1 · 853 Å² buried · 10 hydrogen bonds · protein-protein
K–L · 851 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 33 disulfide, 33 glycan (disulfide, N-glycosylation).

Compared structures

4WJG · Structure of T. brucei haptoglobin-hemoglobin receptor binding to human… · the same entry in another collection · chain K against K, 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
Every structure of UniProt P69905
Every structure of UniProt P68871
Every structure of UniProt P00738
Every structure of UniProt Q99TD3
Every structure of UniProt I7BA80
Elsewhere: RCSB PDB 4WJG · PDBe 4WJG · UniProt P69905 · UniProt P68871 · UniProt P00738 · UniProt Q99TD3 · UniProt I7BA80

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