Citations in PubMed

Primary Citation PubMed: 14603310 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 13

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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Prediction of transmembrane helix orientation in polytopic membrane proteins.

(2006) BMC Struct Biol 6

PubMed: 16792816 | PubMedCentral: PMC1540425 | DOI: 10.1186/1472-6807-6-13

PDB Helix count 1 L ¯ f MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9... 8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacuWGmbatgaqeamaaBaaaleaacqWGMbGzaeqaaaaa@2F66@ Exp 2 L ¯ f MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacuWGmbatgaqeamaaBaaaleaacqWGMbGzaeqaaaaa@2F66@ Brd 3 E ¯ f MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacuWGfbqrgaqeamaaBaaaleaacqWGMbGzaeqaaaaa@2F58@ Exp 2 E ¯ f MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacuWGfbqrgaqeamaaBaaaleaacqWGMbGzaeqaaaaa@2F58@ Brd 3 S f Exp 2 S f Brd 3 1C3W 7 2 2 7 7 7 6 1EUL 9 4 4 8 7 9 7 1FX8 4 1 0 3 3 3 3 1IWG 10 4 4 8 6 7 6 1J4N 4 4 2 3 4 4 4 1KPL 10 4 6 7 8 8 9 1KQF 5 4 2 4 3 5 3 1L9H 7 5 5 7 7 7 7 1M3X 11 7 6 9 6 10 8 1NEK 5 5 2 5 4 5 3 1OCR 24 14 11 18 13 21 11 1OKC 6 2 1 4 3 5 3 1PV6 12 6 3 9 4 9 6 1PW4 12 8 9 8 7 10 11 1Q16 5 3 5 5 3 5 5 1Q90 12 6 4 10 7 11 11 1RH5 9 6 2 7 3 7 3 1ZCD 10 5 3 9 6 10 8 Total 162 100% 90 56% 71 44% 131 81% 102 63% 143 88% 114 70% 1 Number count of lipid-exposed TM helices.

The PDB names for the protein structures used: 1C3W , 1E12 , 1EHK , 1EUL , 1FX8 , 1H2S , 1IWG , 1J4N , 1JB0 , 1K4C , 1KB9 , 1KF6 , 1KPL , 1KQF , 1L7V , 1L9H , 1M3X , 1M56 , 1MSL , 1NEK , 1OCR , 1OKC , 1PP9 , 1PV6 , 1PW4 , 1Q16 , 1QLA , 1Q90 , 1RH5 .

Publication Year: 2006


Automated builder and database of protein/membrane complexes for molecular dynamics simulations.

(2007) PLoS One 2

PubMed: 17849009 | PubMedCentral: PMC1963319 | DOI: 10.1371/journal.pone.0000880

Pore water molecules were generated for PDB:2OAR, 1I78, 1OKC, 1UYN, 1UUN and 1ZLL.

We have applied the insertion method for the proteins that have a cylindrical and regular shape, such as PDB:1GZM (bovine rhodopsin), 1ZLL (human phospholamban pentamer), 1I78 (outer membrane protease OmpT), 2GFP (multidrug transporter EmrD), 1OKC (mitochondrial ADP/ATP carrier), 2OAR (mechanosensitive channel of large conductance), 1UYN (translocator domain of autotransporter NalP).

Publication Year: 2007


Adenine nucleotide translocator transports haem precursors into mitochondria.

(2008) PLoS One 3

PubMed: 18728780 | PubMedCentral: PMC2516936 | DOI: 10.1371/journal.pone.0003070

Using MOE, we attempted to model haem-bovine ANT (PDB code: 1OKC [8] ) protein docking.

Publication Year: 2008


Functional expression of human adenine nucleotide translocase 4 in Saccharomyces cerevisiae.

(2011) PLoS One 6

PubMed: 21532989 | PubMedCentral: PMC3080916 | DOI: 10.1371/journal.pone.0019250

Those sites are highlighted in yellow on the bovine ANT1 structure (Protein Data Bank ID: 1OKC).

Publication Year: 2011


Legionella pneumophila secretes a mitochondrial carrier protein during infection.

(2012) PLoS Pathog 8

PubMed: 22241989 | PubMedCentral: PMC3252375 | DOI: 10.1371/journal.ppat.1002459

(B) The three-dimensional structure of the ADP/ATP carrier from B. taurus (PDB: 1OKC), with the three-fold repeated signature motif color-coded as shown in Figure 1A .

Publication Year: 2012


Insights into the mutation-induced HHH syndrome from modeling human mitochondrial ornithine transporter-1.

(2012) PLoS One 7

PubMed: 22292090 | PubMedCentral: PMC3266937 | DOI: 10.1371/journal.pone.0031048

pdb, and 1okc.

pdb, and 1okc.

pdb and 1okc.

pdb), and 20% (for 1okc.

pdb [50] , and (3) 1okc.

Publication Year: 2012


The tumour metabolism inhibitors GSAO and PENAO react with cysteines 57 and 257 of mitochondrial adenine nucleotide translocase.

(2012) Cancer Cell Int 12

PubMed: 22448968 | PubMedCentral: PMC3349534 | DOI: 10.1186/1475-2867-12-11

The structures were generated from PDB 1OKC using PyMol [ 31 ].

Publication Year: 2012


The ABCs of membrane transporters in health and disease (SLC series): introduction.

Mol Aspects Med 34

PubMed: 23506860 | PubMedCentral: PMC3853582 | DOI: 10.1016/j.mam.2012.12.009

/Bacteria Tetramer FAB fragment 3.2 Å 3NCY Fang et al. (2009) Escherichia coli /Bacteria Dimer – 4 Å 3LRC Gao et al. (2009) l -arginine 3 Å 3L1L... Gao et al. (2010) – 3 Å 3OB6 Kowalczyk et al. (2011) ApcT Methanocaldococcus jannaschii /Bacteria – – 2.32 Å 3GIA Shaffer et al. (2009) FAB fragment 2.48 Å 3GI9 2.59 Å 3GI8 GadC Escherichia coli /Bacteria Dimer – 3.1 Å 4DJK Ma et al. (2012) 

 SLC6 LeuT Eubacterium Aquifex aeolicus /Bacteria – Tricyclic antidepressant (TCA) clomipramine 1.85 Å 2Q6H Singh et al. (2007) l -leucine, Sodium, Imipramine 1.7 Å 2Q72 Mhp1 Microbacterium liquefaciens /Bacteria – –– 3.8 Å 2X79 Shimamura et al. (2010) 

 SLC8/24 NCX_MJ Methanococcus jannaschii /Bacteria – – 1.9 Å 3V5U Liao et al. (2012) SLC9 NhaA Escherichia coli /Bacteria – – 3.45 Å 1ZCD Hunte et al. (2005) SLC10 ASBT NM Neisseria memingitidis /Bacteria – Taurocholate 2.2 Å 3ZUX Hu et al. (2011) SLC13 VcINDY Vibrio cholerae /Bacteria Dimer Citrate 3.2 Å 4F35 Mancusso et al. (2012) SLC14 dvUT Desulfovibrio vulgaris /Bacteria – N,N’ -dimethylurea 2.4 Å 3K3F Levin et al. (2009) SLC15 PepT So Shewanella oneidensis /Bacteria – – 3.6 Å 2XUT Newstead et al. (2011) SLC16 GlpT Escherichia coli /Bacteria – – 3.3 Å 1PW4 Huang et al. (2003) SLC23 UraA Escherichia coli /Bacteria – Uracil 2.8 Å 3QE7 Lu et al. (2011) 

 SLC25 ANT1 Bos taurus /− – Carboxyatractyloside (CATR) 2.2 Å 1OKC Pebay-Peyroula et al. (2003) UCP2 ⁎ Mus musculus /Bacteria – GDP – 2LCK Berardi et al. (2011) 

 SLC28 vcCNT Vibrio cholerae /Bacteria Trimer Uridine 2.4 Å 3TIJ Johnson et al. (2012) SLC30 YiiP Escherichia coli /Bacteria Dimer Zinc 3.8 Å 2QFI Lu et al. (2009) 

 SLC42 AmtB Escherichia coli /Bacteria Trimer – 1.4 Å 1U7G Khademi et al. (2004) Rh Nitrosomonas europaea /Bacteria Trimer Carbon dioxide 1.85 Å 3B9Z Li et al. (2007) 

 SLC47 NorM Vibrio cholerae /Bacteria – – 3.65 Å 3MKT He et al. (2010) ⁎ Structure determined by NMR methods.

Publication Year: null


Probabilistic grammatical model for helix-helix contact site classification.

(2013) Algorithms Mol Biol 8

PubMed: 24350601 | PubMedCentral: PMC3892132 | DOI: 10.1186/1748-7188-8-31

Table 1 Datasets summary Dataset/Class Centroid (PDB) Size Fraction WDG150NR   140 100% c1 1Q90 B119‐128 B194‐203 67 48% c2 1OKC A114‐123 A180‐189 35 25% c3 1J4... A18‐27 A101‐110 23 16% c4 1RH5 A29‐38 C34‐42 15 11% PDBTM150NR   227 100% c1 1Q90 B119‐128 B194‐203 100 44% c2 1OKC A114‐123 A180‐189 60 26% c3 1J4N A18‐27 A101‐110 25 11% c4 1RH5 A29‐38 C34‐42 42 19% Results Cross‐validation of grammar classifiers Leave‐one‐out cross‐validation Performance of single grammar classifiers was analysed in the Leave‐One‐Out Cross‐Validation scheme with the WDG150NR dataset.

Publication Year: 2013


An analysis of oligomerization interfaces in transmembrane proteins.

(2013) BMC Struct Biol 13

PubMed: 24134166 | PubMedCentral: PMC4015793 | DOI: 10.1186/1472-6807-13-21

Its first crystal structure [PDB: 1okc] [ 42 ] did not exhibit any plausible dimerization interfaces, since all of the crystal interfaces where either in an upside-down or head-to-tail orientation.

Publication Year: 2013


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4067143

7 Molecular Modeling Because the crystal structure of human ANT1 is not known, a human ANT1 homology model was created on the basis of the crystal structure of bovine ANT1 [Protein Data Bank (PDB) ent... y 1OKC], 16 using Modeler 17 and VMD 18 with the multiseq plugin 19 of VMD and the STAMP algorithm.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4358699

Missense mutations can be mapped onto the 3D structural homology model of ORC1 [ 81 ], which is based on the structure of the carboxyatractyloside inhibited bovine ADP/ATP carrier (PDB ID 1OKC), to di... play the location of each mutation (Figure  4 ).

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4509712

Simulations using MemProtMD with either the yeast (PDB: 4C9G ; Figure 3 B) ( Ruprecht et al., 2014 ) or the bovine (PDB: 1OKC ) ( Pebay-Peyroula et al., 2003 ) AAC reveal a hig... probability for the (phosphates of) PC molecules at the three binding sites for CL.

Publication Year: 2015