Citations in PubMed

Primary Citation PubMed: 10545325 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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transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels.

(2006) Nucleic Acids Res 34

PubMed: 16844989 | PubMedCentral: PMC1538872 | DOI: 10.1093/nar/gkl205

Formally, NWF consists of (PDB id) 1QJP, 1QJ8, 1THQ, 1P4T, 1I78, 1K24 and 1QD6, and WF of 1A0S, 1AF6, 1PRN, 2OMF, 1E54, 1TLY and 2POR.

Publication Year: 2006


Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.

(2010) Open Biochem J 4

PubMed: 21293729 | PubMedCentral: PMC3032220 | DOI: 10.2174/1874091X01004010083

NMR X-ray PDB entry Chain Number of models PDB entry Chain Resolution (Å) 1 2JQX A 1 1D8C A 2.00 2 1EZO A 10 1ANF A 1.67 3 1AH2 A 18 1IAV A 1.80 4 1TR4 A 20 1UOH A 2.00 5 1BXL A 1 1MAZ A 2.20 ... 2GPQ A 10 1IPB A 2.00 7 1A23 A 1 1A2J A 2.00 8 1MM4 A 20 1THQ A 1.90 9 1GGR A 3 2F3G B 2.13 10 1CRP A 20 1GNP A 2.70 11 1OCA A 20 1W8L A 1.80 12 1NMV A 10 1PIN A 1.35 13 1AX3 A 16 1GPR A 1.90 14 1DF3 A 10 1JV4 A 1.75 15 1B6F A 23 1BV1 A 2.00 16 1EQ0 A 20 1DY3 A 2.00 17 1BVH A 15 1DG9 A 1.90 18 1RCH A 8 1RDD A 2.80 19 6I1B A 1 1I1B A 2.00 20 1BA9 A 36 1MFM A 1.02 21 1XPW A 20 1TVG A 1.60 22 1FXT A 1 1FZY B 1.90 23 1JOK A 1 1SNO A 1.70 24 1CFC A 25 1A29 A 2.74 25 1ORM A 20 1QJ8 A 1.90 26 1PFL A 20 1FIK A 2.30 27 1BLR A 22 1CBQ A 2.20 28 2P3M A 20 2VBS A 3.00 29 1JJJ A 20 1B56 A 2.05 30 1JBH A 20 1CRB A 2.10 31 1TBD A 1 2FUF A 1.45 32 1AEL A 20 1ICM A 1.50 33 1A63 A 10 1A62 A 1.55 34 1IY3 A 1 1IWT A 1.40 35 1CYL A 20 1HIK A 2.60 36 1CEY A 46 1CHN A 1.76 37 2JU3 A 10 1LFO A 2.30 38 1FR0 A 30 1A0B A 2.06 39 1GIO A 10 1AGI A 1.50 40 2PRF A 19 1PRQ A 2.50 41 1MVG A 10 1TVQ A 2.00 42 2AAS A 32 1AQP A 2.00 43 1FSP A 20 1NAT A 2.45 44 1PIR A 1 1P2P A 2.60 45 1IT4 A 1 1FAZ A 1.40 46 1KLV A 20 1GNU A 1.75 47 2JN8 A 20 2ES9 A 2.00 48 1SVQ A 20 1SVY A 1.75 49 1K19 A 20 1KX8 A 2.80 50 1BC4 A 15 1KM8 A 1.90 51 1BNR A 20 1YVS A 2.20 52 1A67 A 16 1CEW I 2.00 53 2NLN A 20 1OMD A 1.85 54 1F40 A 10 1FKB A 1.70 55 1MPH A 50 1BTN A 2.00 56 1N5H A 15 1PFP A 2.30 57 1IYY A 24 1BU4 A 1.90 58 2CZN A 38 2CWR A 1.70 59 1N7T A 20 2H3L B 1.00 60 2EVN A 20 2IL4 A 2.05 61 1GO0 A 10 1H7M A 1.96 62 1M42 A 1 2C9Q A 1.60 63 1IIY A 1 3EZM A 1.50 64 1JNJ A 20 1LDS A 1.80 65 1BEG A 18 1BEO A 2.20 66 1C15 A 16 1CY5 A 1.30 67 1BMW A 38 1WHO A 1.90 68 2JMV A 20 2QSK A 1.00 69 1AFH A 15 1FK0 A 1.80 70 3HSF A 30 2HTS A 1.83 71 1PQX A 10 2FFM A 2.51 72 1L8Y A 30 2HDZ A 2.00 73 2CKU A 15 2CG6 A 1.55 74 1A2S A 1 1CTJ A 1.10 75 1ACA A 20 1HB6 A 2.00 76 1GGR B 3 1POH A 2.00 77 1ACP A 2 1T8K A 1.10 78 1D3Z A 10 1AAR B 2.30 79 1RQS A 20 1CTF A 1.70 80 2AIT A 9 1HOE A 2.00 81 1FD8 A 1 1CC7 A 1.20 82 1K3G A 30 1C75 A 0.97 83 2ORC A 32 1ORC A 1.54 84 1HFG A 1 2FHT A 1.70 85 1ZUG A 20 2CRO A 2.35 86 1BQT A 6 1GZR B 2.0 87 3MEF A 16 1MJC A 2.00 88 2BTT A 20 1RUW A 1.80 89 1QQV A 1 1YU5 X 1.40 90 1LQH A 1 2ASC A 1.10 91 1IJC A 20 1F94 A 0.97 92 1AEY A 15 1SHG A 1.80 93 1ERA A 1 3EBX A 1.40 94 1ROF A 10 1VJW A 1.75 95 1JV8 A 23 1BPI A 1.09 96 1H0T B 40 1LP1 A 2.30 97 1KUN A 20 1KNT A 1.60 98 1GB1 A 60 1PGA A 2.07 99 1BFY A 20 1FHH A 1.50 100 1MBE A 1 1GUU A 1.60 101 1FDM 20 2C0W A 3.20 102 1CCM A 8 1CBN A 0.83 103 1PJF A 27 1QL1 A 3.10 104 1HEV A 6 1Q9B A 1.50 105 1ERC A 20 2ERL A 1.00 106 1KX6 A 20 1GCN A 3.00 107 1CIR B 20 1CIQ B 2.20 108 1V6R A 20 1EDN A 2.18 109 1XGA A 35 1NOT A 1.20 Table 2 Mean RMDS and RMDS 100 Values (Standard Deviations in Parenthesis) Calculated for the Superposed Equivalent X-Ray Protein Structure and NMR Models.

Publication Year: 2010


A graph-theoretic approach for classification and structure prediction of transmembrane ?-barrel proteins.

(2012) BMC Genomics 13 Suppl 2

PubMed: 22537300 | PubMedCentral: PMC3394416 | DOI: 10.1186/1471-2164-13-S2-S5

permutations on E. Coli OmpX [PDB: 1QJ8 ] 8-strand barrel.

A ratio of about 1.31% is found in the case of OmpX [PDB: 1QJ8 ] (see Figure 6 ).

Publication Year: 2012


Modulating lipid dynamics and membrane fluidity to drive rapid folding of a transmembrane barrel.

(2013) Sci Rep 3

PubMed: 23771099 | PubMedCentral: PMC3683699 | DOI: 10.1038/srep01989

Examination of the crystal structure of OmpX (PDB ID: 1QJ8) indicates the presence of a partially buried W140 that forms local polar contacts with Q11 upon protein folding ( Supplementary Fig. 14 ).

Publication Year: 2013


Methionine mutations of outer membrane protein X influence structural stability and beta-barrel unfolding.

(2013) PLoS One 8

PubMed: 24265768 | PubMedCentral: PMC3827151 | DOI: 10.1371/journal.pone.0079351

The OmpX M structure was generated by homology modeling using I-TASSER [64] , with Met residues at positions18, 21, 118 replaced by Leu residues, and 1QJ8 [18] as the starting template.

(A) Cartoon representation of OmpX HN (PDB ID: 1QJ8) generated using PyMol [62] , with the three Met residues at positions 18, 21 and 118, rendered as spheres.

Publication Year: 2013


A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins.

(2004) BMC Bioinformatics 5

PubMed: 15070403 | PubMedCentral: PMC385222 | DOI: 10.1186/1471-2105-5-29

Protein name Number of β-strands PDB code [ 29 ] Organism OmpA 8 1QJP Escherichia coli OmpX 8 1QJ8 Escherichia coli OmpT 10 1I78 Escherichia coli OpcA 10 1K24 Neisseria Meningitidis OmpLA 12 1... D5 Escherichia coli Omp32 16 1E54 Comamonas Acidovorans OmpF 16 2OMF Escherichia coli Porin 16 2POR Rhodobacter capsulatus Porin 16 1PRN Rhodobacter blasticus Sucrose porin 18 1A0S Salmonella typhimurium Maltoporin 18 2MPR Salmonella typhimurium FepA 22 1FEP Escherichia coli FhuA 22 2FCP Escherichia coli FecA 22 1KMO Escherichia coli Table 2 Overall measures of accuracy, obtained in the Self-consistency and in the Jacknife testing.

Publication Year: 2004


Structure of the virulence-associated protein VapD from the intracellular pathogen Rhodococcus equi.

(2014) Acta Crystallogr D Biol Crystallogr 70

PubMed: 25084333 | PubMedCentral: PMC4118825 | DOI: 10.1107/S1399004714012632

One such protein, OmpX (Fig. 6 ▶ a ; PDB code 1qj8 ; Vogt & Schulz, 1999 ▶ ), belongs to a family of membrane proteins that plays roles in (i) bacterial adhesion to, and entry ... nto, mammalian cells and (ii) resistance to attack by the human complement system.

Publication Year: 2014


Differential contribution of tryptophans to the folding and stability of the attachment invasion locus transmembrane ?-barrel from Yersinia pestis.

(2014) Sci Rep 4

PubMed: 25266561 | PubMedCentral: PMC4179465 | DOI: 10.1038/srep06508

a,b PDB ID c Protein a,b # of β-strands d,e # of Trp residues Membrane interface Transmembrane Extra-membrane 1 1P4T NspA 10 (8) 0 - - - 2 2POR Porin 22 (16) 1 1 - - 3 3QRA Ail 9 (8) 2 1 1 - 4... 1QJ8 OmpX 8 (8) 2 1 1 - 5 2LHF OprH 10 (8) 2 2 - - 6 3HW9 OmpF 25 (16) 2 1 1 - 7 1E54 Omp32 24 (16) 2 - 1 1 8 3DZM TtoA 14 (8) 3 1 - 2 9 3FID LpxR 17 (12) 3 - 1 2 10 2X27 OprG 17 (8) 4 4 - - 11 3BRY TbuX 27 (14) 4 2 2 - 12 1K24 OpcA 15 (10) 4 3 1 - 13 1UYN NalP 14 (12) 4 3 - 1 14 1H6S Porin 19 (16) 4 3 1 - 15 3EMO Hia [6 (4)]x3 f 1 1 - - 16 4FQE KdgM 14 (12) 3 2 - 1 17 1UUN MspA [14 (2)]x8 f 4 3 1 - 18 3WI4 PorB [22 (16)]x3 f 4 3 - 1 19 1WP1 OprM [13 (4)]x3 f 4 2 - 2 20 2LME YadA [5 (4)]x3 f 2 1 - 1 a Non-redundant structures were retrieved from PDBTM: Protein Data Bank of Transmembrane Proteins; http://pdbtm.enzim.hu/ .

Publication Year: 2014


Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method.

(2005) BMC Bioinformatics 6

PubMed: 15647112 | PubMedCentral: PMC545999 | DOI: 10.1186/1471-2105-6-7

Protein name Number of β-strands PDB ID Reference Organism NspA 8 1P4T [67] Neisseria Meningitidis OmpX 8 1QJ8 [68] Escherichia coli Pagp 8 1MM4 [69] Escherichia coli OmpA 8 1QJP [50] Escheric... ia coli OmpT 10 1I78 [70] Escherichia coli OpcA 10 1K24 [71] Neisseria Meningitidis Nalp 12 1UYN [41] Neisseria Meningitidis OmpLA 12 1QD5 [72] Escherichia coli Porin 16 2POR [73] Rhodobacter capsulatus Porin 16 1PRN [74] Rhodopseudomonas blastica OmpF 16 2OMF [75] Escherichia coli Osmoporin 16 1OSM [76] Klebsiella pneumoniae Omp32 16 1E54 [77] Comamonas Acidovorans Phosphoporin 16 1PHO [78] Escherichia coli Sucrose porin 18 1A0S [79] Salmonella typhimurium Maltoporin 18 2MPR [80] Salmonella typhimurium FhuA 22 2FCP [46] Escherichia coli FepA 22 1FEP [47] Escherichia coli FecA 22 1KMO [48] Escherichia coli BtuB 22 1NQE [49] Escherichia coli Table 6 The available predictors, used for predicting the transmembrane strands of β-barrel outer membrane proteins.

Publication Year: 2005