Citations in PubMed

Primary Citation PubMed: 11832950 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 8

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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Design of multi-specificity in protein interfaces.

(2007) PLoS Comput Biol 3

PubMed: 17722975 | PubMedCentral: PMC1950952 | DOI: 10.1371/journal.pcbi.0030164

pdb, purple, 1K5D.

Publication Year: 2007


Multiple domain insertions and losses in the evolution of the Rab prenylation complex.

(2007) BMC Evol Biol 7

PubMed: 17705859 | PubMedCentral: PMC1994686 | DOI: 10.1186/1471-2148-7-140

Figure 3 Maximum Likelihood reconstruction of the evolutionary relationships between the LRR domains found in RGGTase a-subunit (red branches) and reference sequences representing other superfamilies ... f LRR domains – L-domain-like, internalin LRR ( 106v ) – green; RNI-like, 28-residue LRR, Ribonucelase inhibitor ( 1A4Y ) – blue; RNI-like, RanGAP1, N-terminal domain( 1K5D ) – purple; outer arm dynein light chain( 1M9L ) – orange; L-domain-like, RabGGTase α-subunit, C-terminal domain ( 1LTX ) – red.

Publication Year: 2007


The Rap-RapGAP complex: GTP hydrolysis without catalytic glutamine and arginine residues.

(2008) EMBO J 27

PubMed: 18309292 | PubMedCentral: PMC2265111 | DOI: 10.1038/emboj.2008.30

PDB codes of structures used for figures Ras-RasGAP (1WQ1), Rho-RhoGAP (1TX4), Ran–RanGAP (1K5D), RapGTP (3RAP), Rheb-GTP (1XTS), Ras-GppNHp (5P21).

Publication Year: 2008


LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs).

(2008) BMC Struct Biol 8

PubMed: 18986514 | PubMedCentral: PMC2645405 | DOI: 10.1186/1472-6807-8-47

PDB codes Protein functions LRR classes InterPro Swiss-Prot Pfam SMART LRRML 2A0Z Immune System T 18 22 7 20 25 1G9U Toxin S 7 15 1 0 15 2FT3 Structural Protein T+S 8 8 5 9 12 1K5D Signaling Protein R... 2 8 0 0 11 1GWB Glycoprotein SDS22 6 6 4 7 8 2P1M Signaling Protein CC 2 16 0 6 18 1OGQ Inhibitor PS 7 10 2 0 10 All listed LRR numbers include N-/C-terminal LRRs.

Publication Year: 2008


SwarmDock and the use of normal modes in protein-protein docking.

(2010) Int J Mol Sci 11

PubMed: 21152290 | PubMedCentral: PMC2996808 | DOI: 10.3390/ijms11103623

For these complexes, 1EER, 1GRN, 1K5D and 1KKL, interface C α RMSD after superimposition of the interface, are 2.44 Å, 1.22 Å, 1.19 Å and 2.20 Å respectively.

Publication Year: 2010


Benchmarking and analysis of protein docking performance in Rosetta v3.2.

(2011) PLoS One 6

PubMed: 21829626 | PubMedCentral: PMC3149062 | DOI: 10.1371/journal.pone.0022477

PDB Difficulty | type N 5 µ (N 5 ) [σ(N 5 )] P success Irmsd Classification PDB Difficulty | type N 5 µ (N 5 ) [σ(N 5 )] P success Irmsd Classification 1K74 rigid-body ... O 2 2.5 [1.1] 0.20 1.63 RB sampling 1EER difficult | O 1 0.9 [1.0] 0.02 2.23 BB sampling 1Z5Y rigid-body | O 2 2.4 [1.1] 0.16 1.14 BB sampling 1FAK difficult | O 1 0.9 [0.9] 0.01 3.30 discrimination 1WEJ rigid-body | A 2 2.2 [1.1] 0.14 2.60 discrimination 1TMQ rigid-body | E 1 0.8 [0.9] 0.01 1.47 RB sampling 1HE8 medium | O 2 2.2 [1.1] 0.13 3.19 BB sampling 1I4D rigid-body | O 1 0.8 [0.9] 0.01 3.13 RB sampling 1ATN difficult | O 2 2.1 [1.2] 0.12 1.53 RB sampling 1RLB rigid-body | O 1 0.8 [0.9] 0.01 3.88 RB sampling 2HQS rigid-body | O 2 2.1 [1.2] 0.13 2.69 BB sampling 1Z0K rigid-body | O 1 0.7 [0.8] 0.00 3.56 BB sampling 1JMO difficult | O 2 2.1 [1.2] 0.11 2.82 BB sampling 1EFN rigid-body | O 1 0.7 [0.8] 0.00 3.58 BB sampling 2O8V rigid-body | E 2 2.1 [1.2] 0.12 3.62 BB sampling 1I9R rigid-body | AB 1 0.6 [0.8] 0.00 0.52 RB sampling 1J2J rigid-body | O 2 2.0 [1.4] 0.14 1.10 BB sampling 1AZS rigid-body | O 0 0.5 [0.9] 0.01 5.41 RB sampling 1NSN rigid-body | AB 2 2.0 [1.2] 0.10 1.15 discrimination 2B42 rigid-body | E 0 0.4 [0.6] 0.00 5.85 RB sampling 1K5D medium | O 2 2.0 [1.1] 0.09 2.87 BB sampling 2BTF rigid-body | O 0 0.3 [0.6] 0.00 4.44 BB sampling 1FQ1 difficult | E 2 1.7 [1.3] 0.08 2.18 RB sampling 1KKL medium | E 0 0.2 [0.5] 0.00 4.60 RB sampling 2AJF rigid-body | O 2 1.7 [1.1] 0.06 1.23 RB sampling 1F51 rigid-body | O 0 0.2 [0.5] 0.00 12.35 BB sampling 1E96 rigid-body | O 1 1.6 [1.1] 0.05 3.38 BB sampling 1KAC rigid-body | O 0 0.1 [0.5] 0.00 4.01 BB sampling 1I2M medium | O 1 1.5 [1.0] 0.03 2.68 BB sampling 1MLC rigid-body | A 0 0.1 [0.4] 0.00 4.31 BB sampling 1QFW rigid-body | AB 1 1.5 [1.1] 0.03 1.93 RB sampling 1S1Q rigid-body | O 0 0.1 [0.3] 0.00 4.37 BB sampling 1GLA rigid-body | O 2 1.5 [1.1] 0.05 2.98 BB sampling 1M10 medium | E 0 0.0 [0.0] 0.00 4.46 BB sampling 1AKJ rigid-body | O 1 1.2 [1.0] 0.02 1.48 BB sampling 1A2K rigid-body | O 0 0.0 [0.0] 0.00 5.20 BB sampling 1EZU rigid-body | E 1 1.2 [1.0] 0.02 2.82 RB sampling 1R8S difficult | O 0 0.0 [0.0] 0.00 5.21 BB sampling 1F34 rigid-body | E 1 1.2 [1.0] 0.02 4.00 RB sampling 1GP2 medium | O 0 0.0 [0.0] 0.00 5.23 BB sampling 1GRN medium | O 1 1.1 [1.0] 0.02 1.24 BB sampling 1IBR difficult | O 0 0.0 [0.0] 0.00 5.46 RB sampling 1NW9 medium | E 1 1.1 [1.0] 0.02 2.33 BB sampling 1BKD difficult | O 0 0.0 [0.0] 0.00 5.62 BB sampling 2H7V medium | O 1 1.1 [1.0] 0.02 3.65 BB sampling 2OT3 difficult | O 0 0.0 [0.0] 0.00 6.00 BB sampling 1GHQ rigid-body | O 1 1.0 [1.0] 0.01 2.69 BB sampling 1FQJ rigid-body | O 0 0.0 [0.0] 0.00 6.48 RB sampling 2NZ8 medium | O 1 1.0 [1.0] 0.02 3.91 BB sampling 1PXV difficult | E 0 0.0 [0.0] 0.00 9.49 BB sampling 1IB1 medium | O 1 1.0 [1.0] 0.01 3.95 discrimination 1H1V difficult | O 0 0.0 [0.0] 0.00 9.96 BB sampling 1K4C rigid-body | AB 1 1.0 [1.1] 0.02 2.15 BB sampling 1Y64 difficult | O 0 0.0 [0.0] 0.00 13.70 discrimination 1EWY rigid-body | E 1 1.0 [1.1] 0.02 3.01 BB sampling 1DQJ rigid-body | A 0 0.0 [0.2] 0.00 6.15 BB sampling 2PCC rigid-body | E 1 1.0 [0.9] 0.01 3.38 discrimination 1ACB medium | E 0 0.0 [0.1] 0.00 4.56 RB sampling 1KLU rigid-body | O 0 0.0 [0.1] 0.00 8.16 BB sampling Unsuccessful docking predictions are classified as cases for which the five lowest-energy decoys did not contain at least three near-native structures.

Publication Year: 2011


Sequence and structural analyses of nuclear export signals in the NESdb database.

(2012) Mol Biol Cell 23

PubMed: 22833565 | PubMedCentral: PMC3442415 | DOI: 10.1091/mbc.E12-01-0046

Crystallographic B -factors and disorder propensity of the NESs Of the 47 experimental NESs in the PDB, the NESs of RanBP1 ( 1K5D ), cyclin D1 ( 3G33 ), STRADα ( 3GNI ), and NPM mutant A ( 2VX... ) are part of constructs used in structure determination, but the NES residues were not modeled in the final structures probably due to high mobility or disorder.

Publication Year: 2012


Protein-protein docking with F(2)Dock 2.0 and GB-rerank.

(2013) PLoS One 8

PubMed: 23483883 | PubMedCentral: PMC3590208 | DOI: 10.1371/journal.pone.0051307

Similarly among the other complexes, only F 2 Dock 2.0 is successful for 1J2J, 2A5T, 2A9K, 2HQS, 3BP8, 1K5D, 1R6Q, 2Z0E, 3CPH and 1ATN.

Publication Year: 2013