Citations in PubMed

Primary Citation PubMed: 6644819 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 9

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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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An in silico approach to map the binding site of doxorubicin on hemoglobin.

(2008) Bioinformation 2

PubMed: 18795113 | PubMedCentral: PMC2533059 | DOI: null

Preparation of the protein target and ligand Known crystal structures of oxy-Hemoglobin (Hb) (PDB Id: 1HHO) was obtained from the Brookhaven Protein Data Bank.

Publication Year: 2008


Structure-based predictive models for allosteric hot spots.

(2009) PLoS Comput Biol 5

PubMed: 19816556 | PubMedCentral: PMC2748687 | DOI: 10.1371/journal.pcbi.1000531

PDB of effector ligand-unbound (inactive state) PDB of effector ligand-bound (active state) Training Data Set Proteins CheY (signal transduction) 3chy 1fqw PurR repressor (transcription factor) 1dbq 1... et Tet repressor (transcription factor) 2trt 1qpi Hemoglobin (carrier protein/enzyme) 4hhb 1hho Phosphofructokinase (enzyme) 6pfk 4pfk phosphoglycerate dehydrogenase (enzyme) 1psd 1yba fructose-1,6-bisphosphatase (enzyme) 1eyj 1eyi Aspartate transcarbamoylase (enzyme) 1rac 1d09 RhoA (signal transduction) 1ftn 1a2b CDC-42 (signal transduction) 1an0 1nf3 glycogen phosphorylase (transcription factor) 1gpb 7gpb Independent Data Set Proteins glucokinase (enzyme) 1v4t 1v4s glutamate dehydrogenase (enzyme) 1nr7 1hwz lac repressor (transcription factor) 1tlf 1efa myosin II (motor protein/enzyme) 1vom 1fmw thrombin (enzyme) 1sgi 1sg8 Since the Michaelis constant, K M , has been shown to be an apparent dissociation constant, taking into account all substrate-bound species of enzyme, and is directly proportional to K S , we may replace K S with K M in (2) [54] .

Publication Year: 2009


Structure of the altitude adapted hemoglobin of guinea pig in the R2-state.

(2010) PLoS One 5

PubMed: 20811494 | PubMedCentral: PMC2927554 | DOI: 10.1371/journal.pone.0012389

Furthermore the position of His97 in human hemoglobin is shown in the T-state (grey, PDB-code: 1A3N, [36] ), R-state (orange, PDB-code: 1HHO, [37] ) and R2-state (light... blue, PDB-code: 1BBB, [10] ).

The guinea pig hemoglobin structure is shown in cartoon representation, which is colored according to the distance between corresponding C α -atoms in guinea pig hemoglobin and the respective conformational state of human hemoglobin in (A) T-state (PDB-code: 1A3N, [36] ), (B) R-state (PDB-code: 1HHO, [37] ) and (C) R2-state (PDB-code: 1BBB, [10] ).

Publication Year: 2010


Game on, science - how video game technology may help biologists tackle visualization challenges.

(2013) PLoS One 8

PubMed: 23483961 | PubMedCentral: PMC3590297 | DOI: 10.1371/journal.pone.0057990

A – Human hemoglobin (PDB id: 1HHO) rendered with a stylized blood effect.

Publication Year: 2013


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


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

This fast operation is able to correctly reorder the vast majority of assemblies checked, however, it can fail with hetero-oligomers (e.g., the biological unit of the PDB ID 1hho) or with complex dihe... ral symmetries.

Publication Year: 2013


Molecular Docking of Known Carcinogen 4- (Methyl-nitrosamino)-1-(3-pyridyl)-1-butanone (NNK) with Cyclin Dependent Kinases towards Its Potential Role in Cell Cycle Perturbation.

(2014) Bioinformation 10

PubMed: 25258489 | PubMedCentral: PMC4166773 | DOI: 10.6026/97320630010526

To validate our in silico study, we considered Human oxy -hemoglobin at 1.25 Å resolution, [PDB ID-1HHO] as a +ve control , which showed binding energy of -6.06 kcal/mol , as the binding of Hu... an oxyhemoglobin with NNK has previously been quantified in tobacco users and is considered as a biochemical marker for uptake of tobacco specific nitrosamines [ 24 ].

To validate the results, we considered Human Oxy-Hemoglobin at 1.25 Å Resolution, [PDB_ID:1HHO] as a +ve control , (binding energy -6.06 kcal/mol ).

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


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4353013

However, we note that when HbO 2 was crystallized from phosphate buffer at pH 8.5, a phosphate ion was bound in the cleft between the α chains, bridging the two Lysα99 side chains (PDB... 1HHO), 113 which are near the FG corner (Figure 11 ).

Figure 11 Superposition of the Hb structures with bound phosphate, aligned via the Cα atoms of both α chains, showing the displacement of the FG region and the F helix between native HbO 2 (orange; PDB 1HHO( 113 )) and the Lysα99-fructosyl derivative (cyan; PDB 3B75( 115 )).

Publication Year: 2014