Citations in PubMed

Primary Citation PubMed: 1328651 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 7

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


Prediction of calcium-binding sites by combining loop-modeling with machine learning.

(2009) BMC Struct Biol 9

PubMed: 20003365 | PubMedCentral: PMC2808310 | DOI: 10.1186/1472-6807-9-72

Table 1 20 apo-holo pairs of calcium-binding proteins for validation Holo structure Apo structure Loop Protein and calcium ID Protein name PDB ID Chain ID PDB ID Chain ID All RMSD (Å) Start En... RMSD (Å) Sequence 1B9AA110 PARVALBUMIN 1B9A A 1B8C A 1.48 51 62 2.68 AQDKSGFIEEDE 1C1R_247 CHYMOTRYPSIN INHIBITOR 2 1C1R A 1AZ8 A 0.60 70 80 0.13 EDNINVV E GN E 1DPO_246 TRYPSIN 1DPO A 1BRB E 0.73 70 80 0.37 E HNINVL E GN E 1DVIB275 CALPAIN 1DVI B 1AJ5 B 2.06 111 121 2.36 AG DD M E VSAT E 1DVIB277 CALPAIN 1DVI B 1AJ5 A 1.75 184 195 0.90 D T D RSGTIGSN E 1F6SB202 ALPHA-LACTALBUMIN 1F6S B 1F6R C 0.86 79 89 0.33 KFL DDD LT DD I 1HAZB1246 BETA-CASOMORPHIN-7 1HAZ B 1FLE E 1.06 70 80 0.23 E HNLNQNNGT E 1I40_305 INORGANIC PYROPHOSPHATASE 1I40 A 1MJW A 0.55 138 146 0.25 F E HYK D L E K 1K94_998 GRANCALCIN 1K94 A 1F4Q B 1.23 130 143 0.68 TVDQDGSGTV E HH E 1K94_999 GRANCALCIN 1K94 A 1F4Q A 1.35 62 72 0.67 AGQDG E V D A EE 1K96A91 S100A6 1K96 A 1K8U A 4.15 24 34 1.45 G D KHTLSKK E L 1KXQB4003 ALPHA-AMYLASE, PANCREATIC 1KXQ B 1KXV A 0.46 165 172 0.17 LL D LAL E K 1NLS_240 CONCANAVALIN A 1NLS A 1DQ0 A 0.31 9 20 0.47 L D TYPNT D IG D P 1NOL_632 HEMOCYANIN (SUBUNIT TYPE II) 1NOL A 1OXY A 0.55 577 584 0.13 V D AVSYCG 1PSH_1 PHOSPHOLIPASE A2 1PSH A 1A3D A 0.61 25 34 1.41 GCYCGRGGSG 1QMDA403 PHOSPHOLIPASE C 1QMD A 1QM6 A 0.20 265 270 0.13 SG E K D A 1QMDA405 PHOSPHOLIPASE C 1QMD A 1QM6 A 0.20 292 299 0.14 M D NPGN D F 2POR_304 PORIN 2POR A 3POR A 1.00 135 145 0.98 S D GKVG E TS ED 3LHM_131 HUMAN LYSOZYME 3LHM A 2LHM A 0.21 83 94 0.40 ALL DD NIA DD VA 5CHY_401 CHEY 5CHY A 3CHY A 0.35 55 63 0.15 IS D WNMPNM PDB ID (PDB code followed by chain identifier and calcium index) and protein names are from PDB (column 1-2).

Publication Year: 2009


GRAPE: GRaphical Abstracted Protein Explorer.

(2010) Nucleic Acids Res 38

PubMed: 20462864 | PubMedCentral: PMC2896102 | DOI: 10.1093/nar/gkq398

An example of a porine protein (PDB ID: 2POR), rendered ( a ) with PyMOL ( 1 ) and ( b ) after abstraction and stylization in GRAPE.

Publication Year: 2010


OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria.

(2011) Nucleic Acids Res 39

PubMed: 20952406 | PubMedCentral: PMC3013764 | DOI: 10.1093/nar/gkq863

Finally, two well-studied porins from Rhodobacter capsulatus (PDB ID:2POR) and Rhodopeudomonas blastica (PDB ID:1PRN) had no hits in the Pfam domains.

Publication Year: 2011


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

These misplaced strands, which belong to the proteins with PDB codes 1PRN and 2POR, were the only strands that have been falsely predicted (false positives).

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 1QD5 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


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