Citations in PubMed

Primary Citation PubMed: 9515969 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 5

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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Hydrogen bonds of DsrD protein revealed by neutron crystallography.

(2008) J Synchrotron Radiat 15

PubMed: 18421158 | PubMedCentral: PMC2394825 | DOI: 10.1107/S0909049507058979

Nine neutron structures {rubredoxin [Protein Data Bank (PDB) id: 1VCX], rebonulcease A (6RSA), myoglobin (1L2K), concanavalin A (1XQN), trypsin (1NPT), dihydrofolate reductase (2INQ), insulin (3INS), ... ysozyme (1IO5), endothiapepsin (1GKT)} and seven X-ray structures [trypsin inhibitor (5PTI), crambin (1EJG), subtilisin (1GCI), anti-freezing protein (1UCS), xylose isomerase (1MUW), endo-1,4-beta-xylanase (1I1W) and photoactive yellow protein (3PYP)] were calculated in the same procedure on HHDB.

Publication Year: 2008


Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures.

(2009) Proteins 75

PubMed: 18814299 | PubMedCentral: PMC3056144 | DOI: 10.1002/prot.22234

For 3PYP:His108, Protonate3D predicted a neutral N ε tautomer whereas the deposited coordinates contained a cationic imidazole.

Glu46 in 3PYP is an interesting case and the single case of a deposited neutral carboxylic acid in the test collection (and in all the 0.85 Å or better resolution crystal structures).

Figure 3 Left is a depiction of the deposited coordinates of 3PYP (photoactive yellow protein) in which Glu46 is neutral and in an unusual conformation and the phenol oxygen of the covalently bound ligand HC4 is apparently anionic.

” Table I X-Ray Crystal Structures Used for Validation and Overall Atomic Agreement Code a Res b (Å) Len c pH d Compound Time e (s) Atoms f Agree g (%) 1EJG 26 0.54 46 7.0 Crambin 0.9 31 87 1GCI 27 0.78 269 5.9 Subtilisin 11.3 185 99 1GDN 28 0.81 242 6.0 Trypsin 19.0 167 85 1P9G 29 0.84 41 5.5 Antifungal protein 0.9 20 90 1UCS 30 0.62 64 7.5 Antifreeze protein RD1 1.3 76 91 1YK4 31 0.69 53 6.0 Rubredoxin 1.5 56 88 2B97 32 0.75 140 7.4 Hydrophobin II 2.2 128 89 2H5C 33 0.82 198 4.3 Alphalytic protease 9.0 163 85 3PYP 34 0.85 125 4.8 Photoactive yellow protein 4.1 119 95 a Superscripts denote manuscript references.

Publication Year: 2009


A comparative study of the second-order hydrophobic moments for globular proteins: the consensus scale of hydrophobicity and the CHARMM partial atomic charges.

(2011) Int J Mol Sci 12

PubMed: 22272083 | PubMedCentral: PMC3257080 | DOI: 10.3390/ijms12128449

residues I Photoactive yellow protein 4 3PYP 125 Exonuclease III 125 1AKO 268 Carboxypeptidase A 39 2CTC 307 Cellulase cela 96 1CEM 363 Myrosinase 55 1E70 499 II Lysozyme 2 3LTZ 129 Dienoyl-coa isomer... se 57 1DCIA 275 Sulfate-Binding protein 139 1SBP 309 Maltodextrin-binding protein 122 3MBP 370 Alpha-amylase 118 1JAE 470 III Cytochrome C′ 108 1CPQ 129 Molybdate transport protein 135 1AMF 231 L-arabinose-binding protein 81 1ABE 305 Phosphate-binding protein 133 2ABH 321 Leucine aminopeptidase 83 1LAM 484 Table 2 Values of ASA (Å 2 ) and the consensus scale for each amino-acid residue.

Publication Year: 2011


Structure of an MmyB-like regulator from C. aurantiacus, member of a new transcription factor family linked to antibiotic metabolism in actinomycetes.

(2012) PLoS One 7

PubMed: 22844465 | PubMedCentral: PMC3406030 | DOI: 10.1371/journal.pone.0041359

The LBD is also similar to the heme PAS sensor protein FixL (PDB ID 1ew0, Z = 6.4, rmsd 3.5 Å for 100 equivalent C α atoms, seq id 10%) [23] , and the photoactive yello... protein PYP [24] (PDB 3pyp, Z = 5.8, rmsd 3.4 Å for 99 equivalent C α atoms, seq id 12%).

Publication Year: 2012


Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences.

(2001) Genome Biol 2

PubMed: 11790254 | PubMedCentral: PMC64836 | DOI: null

A consensus secondary structure was derived from those available for FixL (1EW0) and photoactive yellow protein (3PYP).

Publication Year: 2001