2D5Z: T-state human hemoglobin

Crystal structure of T-state human hemoglobin complexed with three L35 molecules. Determined by X-ray diffraction at 1.45 Å resolution. Released 7 Mar 2006.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,231
Mol. weight: 65.7 kDa
Ligands: HEM, L35
Released: 7 Mar 2006

Explore 2D5Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2D5Z contains 42 α-helices and 0 β-strands across 4 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: 10 helices, 0 β-strands

Element	Residues	Length
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	119-137	19

Chain B: 11 helices, 0 β-strands

Element	Residues	Length
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	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: 10 helices, 0 β-strands

Element	Residues	Length
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 D: 11 helices, 0 β-strands

Element	Residues	Length
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemoglobin alpha subunit	A, C	protein	141	Homo sapiens	P69905 (AlphaFold model)
Hemoglobin beta subunit	B, D	protein	146	Homo sapiens	P68871 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2D5Z_1 Hemoglobin alpha subunit (chains A, C)
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
VHASLDKFLASVSTVLTSKYR

Sequence of entity 2 (B, D), FASTA

>2D5Z_2 Hemoglobin beta subunit (chains B, D)
VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
EFTPPVQAAYQKVVAGVANALAHKYH

Ligands and cofactors

ID	Name	Formula	Copies
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	4
L35	2-[4-({[(3,5-dichlorophenyl)amino]carbonyl}amino)phenoxy]-2-methylpropanoic acid	C17 H16 Cl2 N2 O4	3

Primary citation

R-state haemoglobin with low oxygen affinity: crystal structures of deoxy human and carbonmonoxy horse haemoglobin bound to the effector molecule L35. Yokoyama, T., Neya, S., Tsuneshige, A. et al. J Mol Biol (2006) 356:790-801. DOI 10.1016/j.jmb.2005.12.018 · PubMed

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:…
7DY3 1.4 Å, High resolution crystal structure of hemoglobin M Iwate.
3S66 1.4 Å, Structures and oxygen affinities of crystalline human hemoglobin C (beta6 Lys) in the R…

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