Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 14

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Spontaneous quaternary and tertiary T-R transitions of human hemoglobin in molecular dynamics simulation.

(2010) PLoS Comput Biol 6

PubMed: 20463873 | PubMedCentral: PMC2865513 | DOI: 10.1371/journal.pcbi.1000774

Materials and Methods Simulation setup The initial structures for the simulations starting from the R , R2 , and T state were taken from the protein data bank (PDB codes 1IRD [26] , 1B... B [7] and 2HHB [27] , respectively) and protonated using the pdb2gmx software.

Publication Year: 2010


Optimism, persistence, and our collective crystal ball.

(2010) Am J Trop Med Hyg 83

PubMed: 20595466 | PubMedCentral: PMC2912564 | DOI: 10.4269/ajtmh.2010.10-0107

The Protein Data Bank Data (ID: 2HHB) of Fermi and others 33 were downloaded and displayed using the RCSB Protein Workshop Viewer ( http://www.rcsb.org/pdb/ ).

Publication Year: 2010


In silico modeling of the pore region of a KCNQ4 missense mutant from a patient with hearing loss.

(2012) BMC Res Notes 5

PubMed: 22420747 | PubMedCentral: PMC3374714 | DOI: 10.1186/1756-0500-5-145

In hemoglobin (PDB ID: 2hhb ), the side-chain p K a of His97, which is located in the loop domain between helix3 and helix4 and surrounded by negatively charged residues of Asp94 (located contiguous t... the C-terminus of helix 3) and Asp99 (N-terminus of helix 4) within 5 Å distance, is shifted to an abnormally high value (pK a = 7.8) [ 21 ].

Publication Year: 2012


Protein molecular surface mapped at different geometrical resolutions.

(2013) PLoS One 8

PubMed: 23516572 | PubMedCentral: PMC3597524 | DOI: 10.1371/journal.pone.0058896

Protein name PDB code Atoms Residues Chains 1 1 α lactalbumin 1A4V 1092 123 1 2 2 porcine β-lactoglobulin 1EXS 1248 160 1 3 bovine β-lactoglobulin 1BEB 2473 324 2 3, Subset 3.1... RMSD(129) = 0.6481 4 hen egg-white lysozyme 1LYZ 1001 129 1 5 turkey egg-white lysozyme 135L 994 129 1 6 hen egg-white lysozyme 2LYM 1001 129 1 7 triciclic lysozyme 2LZT 1001 129 1 3, Subset 3.2 RMSD(164) = 0.24 8 mutant of phage T4 lysozyme 1L35 1305 164 1 9 T4 lysozyme 1LYD 1309 164 1 4 RMSD(124) = 0.1655 10 ribonuclease-A 8RAT 951 124 1 11 ribonuclease-A 1RBX 956 124 1 12 bovine ribonuclease-A 3RN3 957 124 1 13 ribonuclease-A 1AFU 1894 248 2 5, Subset 5.1 RMSD(287)  = 0.8877 14 human oxyhemoglobin 1HHO 2192 287 2 15 human carbonmonoxy hemoglobin 2HCO 2192 287 2 16 horse deoxyhemoglobin 2DHB 2201 287 2 5, Subset 5.2 RMSD(574)  = 1.501 17 human hemoglobin A 1BUW 4342 574 4 18 human hemoglobin (W37A) 1Y4F 4368 574 4 19 hemoglobin mutant (W37A) 1A01 4368 574 4 20 human hemoglobin (W37E) 1Y4P 4376 574 4 21 hemoglobin mutant (W37Y) 1A00 4382 574 4 22 human hemoglobin (W37Y) 1Y46 4382 574 4 23 human deoxyhemoglobin 2HHB 4384 574 4 24 human hemoglobin (W37G) 1Y4G 4366 574 4 25 hemoglobin mutant (V1M) 1A0U 4386 574 4 26 hemoglobin mutant (V1M) 1A0Z 4386 574 4 27 recombinant hemoglobin 1C7D 4396 576 3 6 RMSD(585) = 2.3740 28 human serum albumin complexed with octadecanoic acid 1E7I 4496 585 1 29 recombinant human serum albumin 1UOR 4617 585 1 30 human serum albumin 1E78 4302 585 1 31 human serum albumin 1AO6 4600 585 1 32 human serum albumin 1BM0 4600 585 1 7 33 immunoglobulin 1IGY 10002 1294 4 34 immunoglobulin 1IGT 10196 1316 4 35 intact human IgG B12 1HZH 10355 1344 4 To quantify the similarity between the members of a class, for all sets, or subsets, i.e., for lysozyme and hemoglobins, the Root-Mean-Square Deviation (RMSD) has been calculated using the protein structure comparison service Fold at the European Bioinformatics Institute ( http://www.ebi.ac.uk/msd-srv/ssm ).

Publication Year: 2013


Collective dynamics underlying allosteric transitions in hemoglobin.

(2013) PLoS Comput Biol 9

PubMed: 24068910 | PubMedCentral: PMC3777908 | DOI: 10.1371/journal.pcbi.1003232

[24] , PDB id: 2HHB).

Publication Year: 2013


Detecting repetitions and periodicities in proteins by tiling the structural space.

(2013) J Phys Chem B 117

PubMed: 23758291 | PubMedCentral: PMC3807821 | DOI: 10.1021/jp402105j

The length ( L i ) and center ( Z i ) of the selected tile are (a) homodimeric HPV-16 E2c (pdb: 1r8p) L i = 43, Z i = 58.5; (b) deoxy-hemoglobin (pdb: 2hhb) L i = 141, Z i = 71.5 from chain A; (c) the... β-subunit of Thermotoga maritima DNA polymerase III (pdb: 1vpk) L i = 128, Z i = 297; and (d) the processivity factor of Saccharomyces cerevisiae DNA polymerase-δ (pdb: 1plq) L i = 132, Z i = 190.

Publication Year: 2013


BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry.

(2013) BMC Struct Biol 13

PubMed: 24330655 | PubMedCentral: PMC3924234 | DOI: 10.1186/1472-6807-13-32

In this case, the optimal permutation of chains was that in the PDB files, that led to a standard RMSD value of 0.71 Å (5304/5616 Cα atoms), d) Standard superimposition of human deoxyh... moglobin, PDB IDs 1fdh (green) and 2hhb (lilac).

For this application, we chose two PDB IDs that displayed pseudo-symmetry, the human deoxyhemoglobin (reference: 1fdh and target: 2hhb).

Publication Year: 2013


MARTINI bead form factors for the analysis of time-resolved X-ray scattering of proteins.

(2014) J Appl Crystallogr 47

PubMed: 25242909 | PubMedCentral: PMC4119947 | DOI: 10.1107/S1600576714009959

Figure 4 Calculated solution difference scattering between human deoxy and carbonmonoxy hemoglobin crystal models ( 2hhb – 1bbb ), compared with experimental solution data from Cammarata et al... (2008 ▶ ).

In order to estimate the accuracy of difference scattering calculations from coarse-grained structures, the predicted difference scattering between the crystal structures of human deoxy hemoglobin (PDB code 2hhb ; Fermi et al. , 1984 ▶ ) compared with human carbonmonoxy hemoglobin (PDB code 1bbb ; Silva et al. , 1992 ▶ ), as calculated with all-atom and coarse-grained methods, are shown in Fig. 4 ▶ .

Fig. 6 ▶ shows the effect of coarse-graining on X-ray scattering calculations for a hen egg-white lysozyme [PDB code 6lyz (Diamond, 1974 ▶ ); Fig. 6 ▶ ( a )] and human carbon­mon­oxy hemoglobin [PDB code 2hhb , Fig. 6 ▶ ( a )].

The following structures were used (PDB codes in brackets): sperm whale deoxy myoglobin ( 2g0v , second state; Aranda et al. , 2006 ▶ ), sperm whale carbonmonoxy myoglobin ( 2g0r ; Aranda et al. , 2006 ▶ ), human deoxy hemoglobin ( 2hhb ) and human carbonmonoxy hemoglobin ( 1bbb ); these structures were used without cofactors.

Figure 6 ( a ) Determination of q threshold (see text for details) for reliable coarse-grained calculation of protein X-ray scattering for hen egg-white lysozyme (PDB code 6lyz ) and carbonmonoxy hemoglobin (PDB code 2hhb ).

Publication Year: 2014


Green tea potentially ameliorates bisphenol a-induced oxidative stress: an in vitro and in silico study.

(2014) Biochem Res Int 2014

PubMed: 25180096 | PubMedCentral: PMC4142388 | DOI: 10.1155/2014/259763

Preparation of Protein Target Structure and Ligands The X-ray crystal structure of hemoglobin (PDB id-2HHB), catalase (PDB id-1QQW), and glutathione peroxidase (PDB id-2f8A) was retrieved from the Pro... ein Data Bank (PDB ID-2YK0) [ 25 ].

Figure 4 Hydrogen bond and steric interactions of human deoxyhaemoglobin (PDBid-2HHB) with bisphenol A. Green color is bisphenol A and whole structure is hemoglobin.

Virtual Screening Bisphenol A under study was virtually screened (docked) into the binding site of the target proteins as hemoglobin (PDB id-2HHB), catalase (PDB id-1QQW), and glutathione peroxidase (PDB id-2f8A) using ArgusLab 4.0.1 from Planaria Software LLC [ 31 ].

To identify the precise binding sites on hemoglobin, catalase, and glutathione peroxidase, molecular docking simulations were done with the binding mode of bisphenol A. Bisphenol A was docked into the X-ray crystal structures of hemoglobin (PDB id-2HHB), catalase (PDB id-1QQW), and glutathione peroxidase (PDB id-2f8A).

Table 5 Docking results of human erythrocyte (PDB id-2HHB), catalase (PDB id-1QQW), and glutathione peroxidase (PDB id-2F8A) with bisphenol A. Name Target molecules Docking score Interaction H-bond Amino acid interactions H-bond interactions Steric interaction Bisphenol A Hemoglobin −79.5491 −99.0041 −4.80926 Thr 137, Ser 133, Asp 126 Lys 99, Thr 137 Bisphenol A Catalase −36.9179 −54.8291 −3.275 Lys 237, Tyr 215, Ser 201, Tyr 215, Arg 203, Phe 198, Phe 446 Bisphenol A Glutathione peroxidase −71.8106 −86.9671 −3.44834 Arg 20, Glu 111, Glu 114 Phe 110, Glu 114, His 121,

The ligand-binding mode with the lowest energy docking simulations of bisphenol A against proteins (hemoglobin (PDB id-2HHB), catalase (PDB id-1QQW), and glutathione peroxidase (PDB id-2f8A)) were evaluated based on the binding compatibility (docked energy (kcal/mol)) with the receptor (Figures 4 , 5 , and 6 ).

Publication Year: 2014


Role of ?-globin H helix in the building of tetrameric human hemoglobin: interaction with ?-hemoglobin stabilizing protein (AHSP) and heme molecule.

(2014) PLoS One 9

PubMed: 25369055 | PubMedCentral: PMC4219717 | DOI: 10.1371/journal.pone.0111395

The representation was obtained from crystallographic data of oxyHb (2HHB) using the Pymol software.

Publication Year: 2014


Mapping hydrophobicity on the protein molecular surface at atom-level resolution.

(2014) PLoS One 9

PubMed: 25462574 | PubMedCentral: PMC4252106 | DOI: 10.1371/journal.pone.0114042

Protein name PDB code Atoms Residues Chains 1 1 α lactalbumin 1A4V 1092 123 1 2 2 porcine β-lactoglobulin 1EXS 1248 160 1 3 bovine β-lactoglobulin 1BEB 2473 324 2 3 4 chicken e... g-white lysozyme 1LYZ 1001 129 1 5 turkey egg-white lysozyme 135L 994 129 1 6 hen egg-white lysozyme 2LYM 1001 129 1 7 triciclic lysozyme 2LZT 1001 129 1 8 mutant phage T4 lysozyme 1L35 1305 164 1 9 T4 lysozyme 1LYD 1309 164 1 4 10 ribonuclease-A 8RAT 951 124 1 11 ribonuclease-A 1RBX 956 124 1 12 bovine ribonuclease-A 3RN3 957 124 1 13 ribonuclease-A 1AFU 1894 248 2 5 14 human oxyhemoglobin 1HHO 2192 287 2 15 human carbonmonoxy hemoglobin 2HCO 2192 287 2 16 horse hemoglobin 2DHB 2201 287 2 17 human hemoglobin A 1BUW 4342 574 4 18 human hemoglobin 1Y4F 4368 574 4 19 hemoglobin mutant 1A01 4368 574 4 20 human hemoglobin 1Y4P 4376 574 4 21 hemoglobin mutant 1A00 4382 574 4 22 human hemoglobin 1Y46 4382 574 4 23 human deoxyhemoglobin 2HHB 4384 574 4 24 human hemoglobin 1Y4G 4366 574 4 25 hemoglobin mutant 1A0U 4386 574 4 26 hemoglobin mutant 1A0Z 4386 574 4 27 recombinant hemoglobin 1C7D 4396 576 3 6 28 human serum albumin complex with octadecanoic acid 1E7I 4496 585 1 29 recombinant human serum albumin 1UOR 4617 585 1 30 serum albumin 1E_78 4302 585 1 31 human serum albumin 1AO6 4600 585 1 32 human serum albumin 1BM0 4600 585 1 7 33 immunoglobulin 1IGY 10002 1294 4 34 immunoglobulin 1IGT 10196 1316 4 35 intact human IgG B12 1HZH 10355 1344 4 Note: The proteins marked in bold are model proteins and those in italics have been also used for the analysis of statistical strength.

Publication Year: 2014


?-Thalassemia associated with hb instability: a tale of two features. the case of Hb Rogliano or ?1 Cod 108(G15)Thr?Asn and Hb Policoro or ?2 Cod 124(H7)Ser?Pro.

(2015) PLoS One 10

PubMed: 25730315 | PubMedCentral: PMC4346585 | DOI: 10.1371/journal.pone.0115738

B: Cartoon representation of the three-dimensional structure of the αβ dimer from the structure of the tetrameric human deoxy hemoglobin (PDB code 2HHB) [ 23 ].

Structural analysis We evaluated mutation-induced structural alterations by analysing the structure of α-globin chain of human hemoglobin in the complex with AHSP (PDB code 1Y01) and in the tetrameric α2β2 structure (PDB code 2HHB) [ 3 , 23 ].

In particular, in the X-ray structure of human deoxyhemoglobin (PDB code 2HHB), the side chain of the Thr makes an hydrogen bond with the carbonyl oxygen of Cys104α ( Fig. 4A ).

In particular, in the X-ray structure of human deoxy hemoglobin (PDB code 2HHB), the Ser side chain forms a hydrogen bond with the carboxylate OD1 atom of Asp6α and the ND2 atom of Asn9α ( Fig. 4E ).

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4527676

arenicola coelomic Hb structures (PDB: 1hlb, 1hlm) were initially combined with a set of 9 additional Hb structures, representing vertebrate Ngb (1oj6), Cygb (1urv), Mb (2mm1), HbB (2hhb), plant Hbs (... lhl, 2oif), bacterial SDgbs (2wy4, 3s1j), and an invertebrate nerve globin (3mvc).

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4538398

Available at: http://www.rcsb.org/pdb/explore.do?structureId=2HHB .

Publication Year: 2015