MolNFT v1 · #28551 · protein

Crystal structure of riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.

1YHU · Hemoglobin A1 chain: “Crystal structure of riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.”. X-ray diffraction, 3 ligands (HEM, ZN, OXY), 20 pockets (best druggability 0.85). MolNFT v1 #28551 on GenesisL1: 3D…

PDB: 1YHU
Type: protein
Length: 3,516 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemoglobin A1 chain; Giant hemoglobins B chain; Hemoglobin B1A chain; Hemoglobin B2 chain
UniProt: Q8IFK4, P80592, Q8IFK2, Q8IFJ9
Ligands: HEM, ZN, OXY
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I, M, Q, U	Hemoglobin A1 chain	protein	145	77% helix, 0% strand	Q8IFK4
B, F, J, N, R, V	Giant hemoglobins B chain	protein	144	76% helix, 0% strand	P80592
C, G, K, O, S, W	Hemoglobin B1A chain	protein	148	76% helix, 0% strand	Q8IFK2
D, H, L, P, T, X	Hemoglobin B2 chain	protein	149	74% helix, 0% strand	Q8IFJ9

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 24 copies · chains A, C, B, D, E, G, F, H, I, K, J, L, M, O, N, P, Q, S, R, T, U, W, V, X
ZN · Zinc ion · metal · 12 copies · chains B, J, F, N, V, R
OXY · Oxygen molecule · ion · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X

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	965	0.85	0.86	100	HEM, OXY
2	1160	0.85	0.86	122	HEM, OXY
3	1126	0.85	0.86	118	HEM, OXY
4	978	0.84	0.85	70	HEM, OXY
5	948	0.84	0.85	79	HEM, OXY

Interfaces

51 interfaces between chains.

B–D · 1105 Å² buried · 9 hydrogen bonds · protein-protein
N–P · 1098 Å² buried · 9 hydrogen bonds · protein-protein
R–T · 1098 Å² buried · 8 hydrogen bonds · protein-protein
V–X · 1098 Å² buried · 8 hydrogen bonds · protein-protein
J–L · 1097 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

1YHU · Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24… · the same entry in another collection · chain J against J, 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 Q8IFK4
Every structure of UniProt P80592
Every structure of UniProt Q8IFK2
Every structure of UniProt Q8IFJ9
Elsewhere: RCSB PDB 1YHU · PDBe 1YHU · UniProt Q8IFK4 · UniProt P80592 · UniProt Q8IFK2 · UniProt Q8IFJ9

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