Primary Citation PubMed: 16857941
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PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.
(2009) PLoS Comput Biol 5
PubMed: 19609355 | PubMedCentral: PMC2704872 | DOI: 10.1371/journal.pcbi.1000440
(A) KirBac1.1 potassium channel (1p7b); (B) bovine aquaporin-1 (1j4n); (C) KcsA potassium channel (1k4c); (D) MthK calcium-gated potassium channel (1lnq); (E) CorA Mg 2+ transporter (2iub); (F... MscS voltage-modulated mechanosensitive channel (2oau); (G) ASIC1 acid-sensing ion channel (2qts); (H) SecYE-beta protein-conducting channel (2yxr); (I) Kv1.2 voltage-gated potassium channel (2a79); (J) sodium-potassium channel (2ahy); (K) Amt-1 ammonium channel (2b2f); (L) nicotinic acetylcholine receptor (2bg9).
Publication Year: 2009
Initial binding of ions to the interhelical loops of divalent ion transporter CorA: replica exchange molecular dynamics simulation study.
(2012) PLoS One 7
PubMed: 22952795 | PubMedCentral: PMC3431404 | DOI: 10.1371/journal.pone.0043872
The reference structure used is the Chain A of the crystal structure of CorA solved by Eshaghi et al. (PDB code: 2IUB) with the missing residues from Y311 to G326 (sequence: YGMNFEYMPELRWKWG).
Publication Year: 2012
Exploring the structure and function of Thermotoga maritima CorA reveals the mechanism of gating and ion selectivity in Co2+/Mg2+ transport.
(2013) Biochem J 451
PubMed: 23425532 | PubMedCentral: PMC3629940 | DOI: 10.1042/BJ20121745
The structure was solved by the molecular replacement method with PHASER [ 18 ] using the previously solved TmCorA structure (PDB code 2IUB) [ 9 ] as a search model.
The crystal structure (PDB code 2IUB) [ 9 ] revealed Co 2+ binding at the M1 site that is tightly co-ordinated by the carboxyl groups of Asp 89 and Asp 253 .
Publication Year: 2013
Lipid exposure prediction enhances the inference of rotational angles of transmembrane helices.
(2013) BMC Bioinformatics 14
PubMed: 24112406 | PubMedCentral: PMC3854514 | DOI: 10.1186/1471-2105-14-304
Table 7 The list of all protein chains (PDB:Chain) included in the development set and the independent test set Development set Independent test set 1E7P:C 1LNQ:A 1YCE:A 2 F93:A 2PNO:A 2WIT:A ... B8C:A 3EH4:A 2XQ2:A 3MP7:A 1EYS:L 1ORQ:C 1YEW:C 2GFP:A 2Q67:A 2WSW:A 3CHX:A 3EHB:B 2XUT:A 3NYM:A 1EYS:M 1P7B:A 1YQ3:C 2GIF:A 2Q7R:A 2YVX:A 3CHX:B 3G5U:A 3KBC:A 3O0R:B 1FFT:A 1PV6:A 1YQ3:D 2IUB:A 2QJY:A 2Z73:A 3CIR:C 3GIA:A 3KCU:A 3O7P:A 1FFT:B 1PW4:A 1ZCD:A 2JLO:A 2R6G:F 2ZD9:A 3CIR:D 3H90:A 3KG2:A 3OE6:A 1FFT:C 1QLE:C 2A65:A 2NMR:A 2R6G:G 2ZJS:Y 3CN5:A 3H9V:A 3KJ6:A 3ORG:A 1FX8:A 1S5L:B 2AXT:A 2NQ2:A 2R9R:B 2ZW3:A 3D31:C 3HD6:A 3KP9:A 3P4W:A 1GZM:A 1S5L:C 2AXT:D 2NR9:A 2VL0:A 2ZXE:A 3DDL:A 3IJ4:A 3L1L:A 3P5N:A 1JB0:K 1S5L:Z 2BL2:A 2OAR:A 2VPZ:C 3A7K:A 3DHW:A 3JYC:A 3 M71:A 3PJZ:A 1JV6:A 1XIO:A 2C3E:A 2OAU:A 2WDV:C 3B4R:A 3E9J:C 3 K07:A 3MK7:A 1KPK:A 1Y4Z:C 2E75:B 2ONJ:A 2WDV:D 3B5D:A 3EFF:K 3K3F:A 3MK7:C 1KQG:C 3MKT:A Calculation of relative accessible surface area from structures To calculate lipid exposure or exposed area of a structure, we used NACCESS program [ 19 , 29 ] with the probe radius set to 2.0 Å.
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