Citations in PubMed

Primary Citation PubMed: 12297050 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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ErbB2 resembles an autoinhibited invertebrate epidermal growth factor receptor.

(2009) Nature 461

PubMed: 19718021 | PubMedCentral: PMC2762480 | DOI: 10.1038/nature08297

b , Surface representation of a monomer from the EGF-bound s-hEGFR dimer (PDB ID 1ivo) 11 .

Publication Year: 2009

Analysis of conformational variation in macromolecular structural models.

(2012) PLoS One 7

PubMed: 22808083 | PubMedCentral: PMC3392262 | DOI: 10.1371/journal.pone.0039993

PDB ID Region of structural variation Structural manifestations in the variant region PSIPRED Prediction for variant region Disopred Prediction (Residue numbers) 1 3HRY/3K33 50–73: AALDAEFASLF... TLDSTNKELVNR α-helix in complex, turns and coil inindividual protein structure α-helix 72–73 2 3FII/1SFC 27–57: TSNRRLQQTQAQVDEVVDIMRVNVDKVLERD Largely unstructured in one complexand α-helix in another complex α-helix 28–36 3 1N7S/1XTG 167–204: MGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLG α-helix in one complex and largelyunstructured in the other α-helix 167–169, 171–173, 198, 204 4 3C98/3HD7 189–248: KQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAV α-helix in one complex, unstructuredwith distorted helix in another complex α-helix 189, 248 5 2GRX/1IHR 164–182: PARAQALRIEGQVKVKFDV α-helix, β-strand in complex,β-strand in individual protein α-helix, β-strand 164–168 221–235: GSGIVVNILFKINGT Coil and β-strand in complex,β-strand in individual protein β-strand 221, 236 6 2JKR/2BP5 316–325: LAQKIEVRIP β-strand in one complex, unstructuredin the other β-strand 316–319 419–434: IKWVRYIGRSGIYETR β-strand in one complex, unstructuredin the other β-strand 431–434 7 1CDJ/1G9M 54–69: RADSRRSLWDQG α-helix in complex, turn in individualprotein α-helix 58–59, 62–64 12–18: VELTCTA β-strand in individual protein, coilin complex β-strand 12,18 8 3B2V/1IVO 19–32: FEDHFLSLQRMFNN α-helix in one complex and unstructuredin other α-helix 19,32 92–97: YALAVL β-strand in one complex and no electrondensity in other α-helix – 9 1BGW/2RGR 630–682: LQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELI α-helix in complex.

Publication Year: 2012

Molecular determinants of epidermal growth factor binding: a molecular dynamics study.

(2013) PLoS One 8

PubMed: 23382875 | PubMedCentral: PMC3554757 | DOI: 10.1371/journal.pone.0054136

The crystal structures for the sEGFR dimer structure bound to two EGF molecules (PDB code: 1IVO) were used as a starting model for the docking of each ligand.

g007 Figure 7 A Conserved arginine in loop 3 is important for EGFR ligand binding a) Arg41 forms a salt bridge in the EGF-EGFR x-ray structures (PDB IDs 1IVO and 3NJP) with Asp355.

The initial extracellular dimer crystal structure bound to two EGF molecules (PDB id 1IVO) was used [6] .

Ligand Number of residues in structure PDB code Method R.M.S.D. (Å) * Binding affinity (K d ) EGF 47 1IVO X-ray 0.00 0.6 nM AR 50 2RNL NMR 1.45 350 nM BTC 50 1IPO NMR 4.00 1.4 nM EPR 46 1K37 NMR 1.90 2.8 µM *** HB-EGF 40 1XDT X-ray 0.93 7.1 nM EPG 42 Q6UW88 ** Homology 2.05 >500 nM TGF-α 50 1MOX X-ray 3.09 9.2 nM * : Root mean square deviation relative to EGF in 1IVO structure, ** : SWISS-MODEL repository code for homology model database [41] , [42] , *** : Murine Epiregulin.

Publication Year: 2013

Her2 activation mechanism reflects evolutionary preservation of asymmetric ectodomain dimers in the human EGFR family.

(2013) Elife 2

PubMed: 23878723 | PubMedCentral: PMC3713454 | DOI: 10.7554/eLife.00708

By the same measurement, the two crystal structures of the 2-ligand EGFR homodimer (PDB entries 1IVO and 1MOX) differ from one other by 4.0 Å.

Publication Year: 2013

Development of an epidermal growth factor derivative with EGFR blocking activity.

(2013) PLoS One 8

PubMed: 23935985 | PubMedCentral: PMC3728333 | DOI: 10.1371/journal.pone.0069325

g001 Figure 1 Ribbon diagram of the crystal structure of an EGFR homodimer in complex with two EGF ligands (from pdb code 1IVO).

Publication Year: 2013

Structure of the fibrillin-1 N-terminal domains suggests that heparan sulfate regulates the early stages of microfibril assembly.

(2013) Structure 21

PubMed: 24035709 | PubMedCentral: PMC3794157 | DOI: 10.1016/j.str.2013.08.004

(D) Wnt inhibitory factor-1 (WIF-1) EGF2-EGF3 (PDB ID 1IVO ).

Publication Year: 2013

Computational design of binding proteins to EGFR domain II.

(2014) PLoS One 9

PubMed: 24710267 | PubMedCentral: PMC3977815 | DOI: 10.1371/journal.pone.0092513

Subsequently, we conducted a protein docking simulation using the untethered monomer structure of EGFR, specifically chain A of the crystal structure of EGFR (Protein Data Bank [PDB] ID: 1IVO), to sel... ct scaffolds from the scaffold library with a surface shape complementary to EGFR domain II.

Screening scaffolds with shapes complementary to EGFR domain II To screen the scaffolds for shapes complementary to EGFR domain II, docking simulations between each scaffold in the library and the A chain of the human EGFR extracellular domain (RCSB PDB ID: 1IVO) [26] were conducted using PatchDock (version 1.3) [31] , [32] .

This residue numbering is consistent with the RCSB PDB structure of EGFR (1IVO).

Publication Year: 2014

Membrane interaction of bound ligands contributes to the negative binding cooperativity of the EGF receptor.

(2014) PLoS Comput Biol 10

PubMed: 25058506 | PubMedCentral: PMC4109842 | DOI: 10.1371/journal.pcbi.1003742

(A) The staggered and flush conformations [20] are observed in PDB entries 1IVO and 1MOX, respectively.

Publication Year: 2014

Brucine suppresses colon cancer cells growth via mediating KDR signalling pathway.

(2013) J Cell Mol Med 17

PubMed: 23905676 | PubMedCentral: PMC4159018 | DOI: 10.1111/jcmm.12108

The docking study was performed with Sybyl/Surflex module, and the residues in a radius of 6.5 Å around the (PDB ID: 1IVO) were selected as the active site.

Fig. 3 Docking simulation of brucine with KDR (PDB ID 1IVO) was carried out with Surflex.

Publication Year: 2013

Modulating the structure of EGFR with UV light: new possibilities in cancer therapy.

(2014) PLoS One 9

PubMed: 25386651 | PubMedCentral: PMC4227675 | DOI: 10.1371/journal.pone.0111617

In Figure 2B is displayed the 3D structure of the EGFR dimer (1ivo.

Materials and Methods Structure Analysis The crystallography data used for the display of the 3D protein structure ( Figure 2 ) was extracted from 1ivo.

(A) Crystal structure of EGFR extracellular domain (1ivo.

(B) Crystal structure of a 1∶1 complex between human EGF and the dimeric form of EGFR extracellular domain (1ivo.

Results Three-dimensional structure of monomeric and dimeric sEGFR In Figure 2A is displayed the 3D structure of monomeric sEGFR (1ivo.

Publication Year: 2014

Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions.

(2014) BMC Bioinformatics 15

PubMed: 25231912 | PubMedCentral: PMC4262234 | DOI: 10.1186/1471-2105-15-305


Table 1 Uniprot Proteins containing a disulphide-bonded loop comprising over 50% of a PDB protein-protein interface Uniprot Protein containing Interacting PDB ID accession disulphide-bonded loop protein P02462 Collagen alpha-1(IV) chain [Cleaved into: Arresten], Homo sapiens Homodimer 1LI1 Q7T1K6 Natrin-1 (Cysteine-rich venom protein 1) (NA-CRVP1) (Protein G2a), Naja atra Homodimer 1XTA P01133 Pro-epidermal growth factor (EGF) [Cleaved into: Epidermal growth factor (Urogastrone)], Homo sapiens EGF Receptor (ErbB1), Homo sapiens 1IVO P01058 Bowman-Birk type proteinase inhibitor, Phaseolus angularis Bovine trypsin 1TAB P01062 Bowman-Birk type trypsin inhibitor, Vigna radiata Trypsin, Bos taurus 1G9I P17734 Bowman-Birk type seed trypsin and chymotrypsin inhibitor (BTCI), Vigna unguiculata Trypsin, Bos taurus 2G81 P0AD59 Inhibitor of vertebrate lysozyme, Escherichia coli Lysosome C, Gallus gallus 1GPQ Q9JHF9 Lymphocyte antigen 96 (Ly-96) (ESOP-1) (Protein MD-2), Mus musculus Toll-like receptor 4 (TLR-4), Mus musculus 2Z64 A0S865 Irditoxin subunit B (IrTxB), Boiga irregularis Iridotoxin subunit A 2H7Z P50897 Palmitoyl-protein thioesterase 1 (PPT-1) (EC (Palmitoyl-protein hydrolase 1), Homo sapiens Homodimer 3GRO P04004 Somatomedin-B subunit of Vitronectin (VN), Homo sapiens Plasminogen activator inhibitor-1 (PAI-1), Homo sapiens 1OC0 P04004 Somatomedin-B subunit of Vitronectin (VN), Homo sapiens Urokinase plasminogen activator surface receptor (uPAR), Homo sapiens 3BT2 Q03405 Urokinase plasminogen activator surface receptor (uPAR), Homo sapiens Urokinase-type plasminogen activator (uPA), Homo sapiens 3BT2 Q8RS40 Beta-1,3-xylanase (txyA), Alcaligenes sp.

Publication Year: 2014

Ligand binding and dynamics of the monomeric epidermal growth factor receptor ectodomain.

(2013) Proteins 81

PubMed: 23760854 | PubMedCentral: PMC4282322 | DOI: 10.1002/prot.24339

The starting structure for bI was taken from PDBid 1NQL, 2 which is a crystal structure of the monomeric tethered hEGFR ectodomain with EGF bound to domain I. To construct the configuration where EGF ... s attached to domain III, we fitted domain III of PDBid 1IVO 5 to 1NQL and transferred the ligand coordinates.

Publication Year: 2013

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4368709

The structure visualization was based on Protein Data Bank structure models 1nql, 1ivo, 2jwa, 1m17 and 2gs6[ 47 – 50 ].

Publication Year: 2015