7DY3: Hemoglobin M Iwate
High resolution crystal structure of hemoglobin M Iwate. Determined by X-ray diffraction at 1.4 Å resolution. Released 26 Jan 2022.
- Method
- X-ray diffraction
- Resolution
- 1.4 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 11,127
- Mol. weight
- 129.19 kDa
- Ligands
- HEM
- Released
- 26 Jan 2022
Explore 7DY3 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7DY3 contains 86 α-helices and 0 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-17 | 14 | |
| α-helix | 18-20 | 3 | |
| α-helix | 21-35 | 15 | |
| α-helix | 37-42 | 6 | |
| α-helix | 53-71 | 19 | |
| α-helix | 73-75 | 3 | |
| α-helix | 76-79 | 4 | |
| α-helix | 81-86 | 6 | |
| α-helix | 87-91 | 5 | |
| α-helix | 95-112 | 18 | |
| α-helix | 119-137 | 19 | |
Chain B: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 20-34 | 15 | |
| α-helix | 36-45 | 10 | |
| α-helix | 51-56 | 6 | |
| α-helix | 58-74 | 17 | |
| α-helix | 75-77 | 3 | |
| α-helix | 81-90 | 10 | |
| α-helix | 91-95 | 5 | |
| α-helix | 101-118 | 18 | |
| α-helix | 119-121 | 3 | |
| α-helix | 124-142 | 19 | |
Chain C: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-17 | 14 | |
| α-helix | 18-20 | 3 | |
| α-helix | 21-35 | 15 | |
| α-helix | 37-42 | 6 | |
| α-helix | 53-71 | 19 | |
| α-helix | 73-75 | 3 | |
| α-helix | 76-79 | 4 | |
| α-helix | 81-86 | 6 | |
| α-helix | 87-91 | 5 | |
| α-helix | 96-112 | 17 | |
| α-helix | 119-137 | 19 | |
Chain D: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 23-34 | 12 | |
| α-helix | 36-45 | 10 | |
| α-helix | 51-56 | 6 | |
| α-helix | 58-75 | 18 | |
| α-helix | 81-90 | 10 | |
| α-helix | 91-95 | 5 | |
| α-helix | 101-118 | 18 | |
| α-helix | 119-121 | 3 | |
| α-helix | 124-142 | 19 | |
Chain E: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-17 | 14 | |
| α-helix | 18-20 | 3 | |
| α-helix | 21-35 | 15 | |
| α-helix | 37-42 | 6 | |
| α-helix | 53-71 | 19 | |
| α-helix | 73-75 | 3 | |
| α-helix | 76-79 | 4 | |
| α-helix | 81-86 | 6 | |
| α-helix | 87-91 | 5 | |
| α-helix | 96-112 | 17 | |
| α-helix | 119-136 | 18 | |
Chain F: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 20-34 | 15 | |
| α-helix | 36-41 | 6 | |
| α-helix | 43-45 | 3 | |
| α-helix | 51-56 | 6 | |
| α-helix | 58-74 | 17 | |
| α-helix | 75-77 | 3 | |
| α-helix | 81-94 | 14 | |
| α-helix | 101-118 | 18 | |
| α-helix | 119-121 | 3 | |
| α-helix | 124-142 | 19 | |
Chain G: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-17 | 14 | |
| α-helix | 18-20 | 3 | |
| α-helix | 21-35 | 15 | |
| α-helix | 37-42 | 6 | |
| α-helix | 53-71 | 19 | |
| α-helix | 76-79 | 4 | |
| α-helix | 81-86 | 6 | |
| α-helix | 87-91 | 5 | |
| α-helix | 96-112 | 17 | |
| α-helix | 119-136 | 18 | |
Chain H: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 23-34 | 12 | |
| α-helix | 36-45 | 10 | |
| α-helix | 51-56 | 6 | |
| α-helix | 58-75 | 18 | |
| α-helix | 78-80 | 3 | |
| α-helix | 81-90 | 10 | |
| α-helix | 91-95 | 5 | |
| α-helix | 101-118 | 18 | |
| α-helix | 119-121 | 3 | |
| α-helix | 124-142 | 19 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Hemoglobin subunit alpha | A, C, E, G | protein | 141 | Homo sapiens | P69905 (AlphaFold model) |
| Hemoglobin subunit beta | B, D, F, H | protein | 146 | Homo sapiens | P68871 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G), FASTA
>7DY3_1 Hemoglobin subunit alpha (chains A, C, E, G)
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
KVADALTNAVAHVDDMPNALSALSDLYAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
VHASLDKFLASVSTVLTSKYR
Sequence of entity 2 (B, D, F, H), FASTA
>7DY3_2 Hemoglobin subunit beta (chains B, D, F, H)
VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
EFTPPVQAAYQKVVAGVANALAHKYH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| HEM | Protoporphyrin IX containing FE | C34 H32 Fe N4 O4 | 8 |
Primary citation
High resolution crystal structure of hemoglobin M Iwate. Nagatomo, S., Naoya, S., Ohki, M. et al. To be published.
Other PDB entries of the same protein (UniProt P69905 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2W72 1.07 Å, Deoxygenated structure of a distal site hemoglobin mutant plus xe
- 1IRD 1.25 Å, Crystal Structure of Human Carbonmonoxy-Haemoglobin at 1.25 A Resolution
- 2DN1 1.25 Å, 1.25A resolution crystal structure of human hemoglobin in the oxy form
- 2DN2 1.25 Å, 1.25A resolution crystal structure of human hemoglobin in the deoxy form
- 2DN3 1.25 Å, 1.25A resolution crystal structure of human hemoglobin in the carbonmonoxy form
- 7DY4 1.3 Å, High resolution crystal structure of hemoglobin M Boston.
- 6KA9 1.4 Å, Crosslinked alpha(Fe-CO)-beta(Ni) human hemoglobin A in the T quaternary structure at 95…
- 6KAO 1.4 Å, Carbonmonoxy human hemoglobin C in the R quaternary structure at 95 K: Dark
- 6LCW 1.4 Å, Crosslinked alpha(Ni)-beta(Ni) human hemoglobin A in the T quaternary structure at 95 K:…
- 6LCX 1.4 Å, Crosslinked alpha(Ni)-beta(Ni) human hemoglobin A in the T quaternary structure at 95 K:…
- 3S66 1.4 Å, Structures and oxygen affinities of crystalline human hemoglobin C (beta6 Lys) in the R…
- 1J40 1.45 Å, Direct observation of photolysis-induced tertiary structural changes in human…
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