Citations in PubMed

Primary Citation PubMed: 10494852 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 4

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.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

Sequence analysis and structure prediction of type II Pseudomonas sp. USM 4-55 PHA synthase and an insight into its catalytic mechanism.

(2006) BMC Struct Biol 6

PubMed: 17076907 | PubMedCentral: PMC1636056 | DOI: 10.1186/1472-6807-6-23

Method Template Fold % id Score 3DPSSM Human Gastric Lipase (PDB id: 1HLG) α/β hydrolase fold 11 E value a = 0.00888 Human soluble epoxide hydrolase (PDB id: 1S8O) α/β ... ydrolase fold 14 E value = 0.327 Bromoperoxidase (PDB id: 1BRT) α/β hydrolase fold 11 E value = 0.519 mGenThreader Haloalkane Dehalogenase (PDB id: 1BN6:A) α/β hydrolase fold 11 E value b = 3e-05 Mouse Epoxide Hydrolase (PDB id: 1CR6:A) α/β hydrolase fold 8 E value = 3e-05 Human Gastric Lipase (PDB id: 1HLG:A) α/β hydrolase fold 11 E value = 3e-05 FUGUE Human Gastric Lipase (PDB id: 1HLG:A) α/β hydrolase fold 11 Z-SCORE c = 7.86 Hydroxynitrile-Lyase (PDB id: 1QJ4) α/β hydrolase fold 11 Z-SCORE = 6.31 Proline Iminopeptidase (PDB id: 1AZW) α/β hydrolase fold 12 Z-SCORE = 5.08 a E-value must be as low as possible b E-value < 0.001; very significant and certain c Recommended cutoff : Z-SCORE >= 6.0 (CERTAIN 99% confidence) Table 2 Comparison of the Cα distances for the catalytic residues between the template structure 1HGL and the predicted structure of PhaC1 P.sp USM 4–55 Catalytic Residues PhaC1 P.sp USM 4–55 1HLG Nucleophile – Histidine Cys296 – His479 = 7.95 Å Ser153 – His353 = 7.41 Å Histidine – Acid His479 – Asp451 = 4.74 Å His353 – Asp324 = 4.67 Å

Publication Year: 2006


Analysis of the distribution of functionally relevant rare codons.

(2008) BMC Genomics 9

PubMed: 18457591 | PubMedCentral: PMC2391168 | DOI: 10.1186/1471-2164-9-207

of sequences PDB-entry abH01.02 Mammalian carboxylesterases 10 9 1K4Y abH08.14 Ccg1/TafII250-interacting factor B like 2 9 1IMJ abH09.02 BioH protein like 0 10 1M33 abH12.01 Hydroxynitrile lyases 3 10... 1QJ4 abH14.02 Gastric lipases 0 10 1HLG abH15.02 Burkholderia cepacia lipase like 6 7 4LIP abH17.01 Chloroflexus aurantiacus lipase like 3 7 - abH19.01 Palmitoyl-protein thioesterase 1 like 4 8 1EXW abH23.01 Rhizomucor mihei lipase like 0 10 1DU4 abH24.01 Pseudomonas lipases 2 8 - abH26.01 Deacetylases 0 7 1ODT abH28 Prolyl endopeptidases 0 9 1O6F abH30.01 Cocaine esterases 0 8 1L7Q abH31.02 Carboxymethylenebutenolidases 0 8 1DIN abH33.01 Antigen 85-C 0 10 1DQZ abH34.02 Serine carboxypeptidase II like 7 9 1GXS All families are listed with their internal unique identifier (LED ID), their family name, the number of predicted RCRRs, the number of sequences in this family, and the PDB entry used to assign predicted RCRRs to secondary structure elements.

Publication Year: 2008


Beyond rotamers: a generative, probabilistic model of side chains in proteins.

(2010) BMC Bioinformatics 11

PubMed: 20525384 | PubMedCentral: PMC2902450 | DOI: 10.1186/1471-2105-11-306

Structure L, B a Lennard-Jones b BASILISK c BASILISK BB d IRECS e SCWRL 4 e χ 1 (%) χ 2 | χ 1 (%) f χ 1 (%) χ 2 | χ 1 (%) f χ 1 (%) χ 2 ... χ 1 (%) f χ 1 (%) χ 2 | χ 1 (%) f χ 1 (%) χ 2 | χ 1 (%) f 1NAR 289, 45 77.78 76.92 73.33 87.50 93.33 87.50 84.44 70.37 86.67 79.31 5P21 166, 21 90.48 77.78 85.71 100.00 95.24 88.89 95.24 88.89 100.00 80.00 1BJ7 150, 12 91.67 75.00 100.00 77.78 100.00 77.78 91.67 75.00 83.33 85.71 1GCI 269, 40 95.00 86.67 97.50 81.25 100.00 81.25 95.00 85.71 97.50 93.33 2BAA 243, 30 86.67 60.00 83.33 86.67 90.00 82.35 86.67 81.25 90.00 94.12 1DHN 121, 15 93.33 100.00 100.00 85.71 86.67 100.00 93.33 100.00 93.33 100.00 1AMM 174, 22 90.91 100.00 100.00 92.86 100.00 92.86 100.00 85.71 86.36 90.91 1IC6 279, 47 89.36 73.68 91.49 70.00 93.62 75.00 91.49 73.68 93.62 85.00 1KOE 172, 26 80.77 92.86 73.08 84.62 80.77 84.62 92.31 92.86 88.46 84.62 2HVM 273, 43 83.72 74.07 95.35 82.76 90.70 89.66 90.70 85.19 90.70 84.62 3LZT 129, 10 80.00 83.33 70.00 83.33 80.00 83.33 100.00 83.33 100.00 83.33 1CEX 197, 24 95.83 89.47 100.00 100.00 95.83 100.00 87.50 94.74 100.00 100.00 1AGY 197, 25 92.00 84.21 96.00 100.00 96.00 100.00 84.00 94.74 92.00 100.00 1EDG 380, 76 85.53 65.85 85.53 85.00 90.79 81.82 85.53 80.49 89.47 86.05 1THV 207, 20 85.00 76.92 80.00 91.67 85.00 92.31 90.00 76.92 90.00 100.00 2CPL 164, 24 95.83 73.33 91.67 85.71 95.83 93.33 100.00 80.00 95.83 93.33 1NPK 150, 16 100.00 60.00 100.00 80.00 100.00 90.00 93.75 88.89 87.50 88.89 1MLA 305, 38 97.37 71.43 97.37 86.36 100.00 86.36 94.74 75.00 92.11 84.21 1ARB 263, 37 89.19 90.48 89.19 88.89 86.49 85.00 86.49 68.42 83.78 90.00 1MML 251, 19 78.95 81.82 84.21 75.00 89.47 91.67 94.74 83.33 94.74 91.67 1CHD 198, 26 96.15 68.75 96.15 81.25 100.00 76.47 92.31 73.33 92.31 80.00 1QQ4 198, 25 80.00 60.00 84.00 80.00 84.00 90.91 88.00 63.64 88.00 81.82 1QJ4 256, 36 83.33 75.00 91.67 81.48 94.44 81.48 91.67 85.71 94.44 81.48 1B9O 123, 14 78.57 50.00 71.43 57.14 78.57 50.00 92.86 66.67 92.86 44.44 1BYI 224, 30 80.00 86.67 100.00 100.00 96.67 94.12 90.00 87.50 93.33 100.00 1XNB 185, 22 90.91 91.67 100.00 91.67 95.45 100.00 100.00 66.67 95.45 91.67 2PTH 193, 19 94.74 100.00 100.00 100.00 94.74 100.00 94.74 100.00 100.00 100.00 1WHI 122, 12 91.67 100.00 100.00 75.00 100.00 75.00 91.67 100.00 100.00 100.00 153L 185, 26 84.62 93.33 96.15 93.33 88.46 86.67 100.00 87.50 100.00 100.00 1QTW 285, 35 94.29 84.00 91.43 91.67 91.43 83.33 88.57 70.83 97.14 80.77 2IHL 129, 12 66.67 75.00 75.00 75.00 83.33 75.00 100.00 75.00 100.00 75.00 1CZ9 139, 14 85.71 88.89 85.71 100.00 100.00 100.00 100.00 88.89 100.00 100.00 2RN2 155, 11 90.91 87.50 90.91 87.50 90.91 100.00 81.82 100.00 81.82 100.00 1RCF 169, 28 92.86 87.50 96.43 82.61 100.00 95.83 82.14 80.00 92.86 90.91 7RSA 124, 12 75.00 100.00 75.00 100.00 75.00 100.00 75.00 100.00 91.67 100.00 1A8Q 274, 39 87.18 70.00 71.79 93.75 89.74 80.95 94.87 87.50 92.31 95.65 1CEM 363, 55 89.09 64.52 83.64 77.42 94.55 79.41 89.09 80.00 89.09 80.00 1AAC 105, 13 100.00 75.00 100.00 100.00 100.00 100.00 92.31 87.50 100.00 87.50 1PLC 99, 10 100.00 85.71 90.00 66.67 100.00 71.43 90.00 85.71 100.00 71.43 1BD8 156, 11 81.82 100.00 90.91 85.71 90.91 100.00 100.00 100.00 90.91 85.71 1NLS 237, 23 78.26 85.71 86.96 87.50 86.96 81.25 86.96 80.00 91.30 81.25 1IXH 321, 44 81.82 72.00 84.09 84.62 88.64 85.19 93.18 75.00 88.64 84.00 1AKO 268, 35 77.14 72.73 85.71 91.30 85.71 91.30 100.00 81.48 97.14 88.46 Average 207, 27 87.44 80.65 89.32 86.25 92.08 87.49 91.92 83.43 93.13 88.26 The table shows the percentage of correctly predicted χ angles for the different MCMC experiments.

Publication Year: 2010


Hydroxynitrile lyases with ?/?-hydrolase fold: two enzymes with almost identical 3D structures but opposite enantioselectivities and different reaction mechanisms.

(2012) Chembiochem 13

PubMed: 22851196 | PubMedCentral: PMC3444685 | DOI: 10.1002/cbic.201200239

A homology model of At HNL was built using the program MODELLER 8v1, 39 based on structures of the HNLs from H. brasiliensis ( Hb HNL, PDB ID: 1QJ4) and M. esculenta ( Me HNL, PDB ID: 1DWP) as well as... of the salicylic-acid-binding protein from tobacco (PDB ID: 1XKL) as templates.

With an root-mean-square deviation of 0.8 Å (for the superposition of 237 out of 258 Cα-atoms) the structure of At HNL is indeed very similar to that of the HNL from H. brasiliensis ( Hb HNL, PDB ID: 1QJ4).

Publication Year: 2012