Citations in PubMed

Primary Citation PubMed: 12563259 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 4

Citations in PubMed

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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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Structure and binding kinetics of three different human CD1d-alpha-galactosylceramide-specific T cell receptors.

(2006) J Exp Med 203

PubMed: 16520393 | PubMedCentral: PMC2118257 | DOI: 10.1084/jem.20052369

There are currently five unique mouse αβ TCR structures in the PDB, four of them are complexes with pMHC class I (accession nos.: 2CKB, 1FO0, 1KJ2, and 1NAM ), three more are TCR struc... ures alone ( 1TCR, 1NFD, and 1KB5 ), of these 1TCR and 1KB5 are also the TCR part in 2CKB and 1KJ2, respectively.

Publication Year: 2006


pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes.

(2010) Immunome Res 6 Suppl 1

PubMed: 20875153 | PubMedCentral: PMC2946780 | DOI: 10.1186/1745-7580-6-S1-S2

Amongst the results from single template docking experiments, the most accurate docked conformation of the least energy peptide, with a Cα RMSD of 0.06 Å compared to its relevant PDB p... ptide structure (Table 4 ), was achieved for the peptide from the structure 1kbg docked onto the MHC from the structure 1nam having the same murine MHC allele (H2-Kb) as the complex 1kbg.

MHC class Peptide PDB Allele Peptide PDB MHC Template Structure Template Allele Peptide Length Peptide Sequence Cα RMSD (Å) Previous method pDOCK I HLA-A*0201 2v2w 1qrn HLA-A*0201 9 SLYNTVATL 0.63 0.38 I HLA-A*0201 1hhh 1qrn HLA-A*0201 10 F LPSDFFPSV 0.58 0.25 I HLA-A*0201 1qse 1qrn HLA-A*0201 9 LLFGYPRYV 0.62 0.30 I HLA-A*0201 2bnq 1qrn HLA-A*0201 9 SLLMWITQV 0.97 0.77 I HLA-A*0201 2gj6 1qrn HLA-A*0201 9 LLFGKPVYV 0.56 0.24 I HLA-A*0201 1qr1 1qrn HLA-A*0201 9 IISAVVGIL 0.87 0.36 I HLA-A*0201 1qsf 1qrn HLA-A*0201 9 LLFGYPVAV 0.94 0.41 I HLA-A*0201 1bd2 1qrn HLA-A*0201 9 LLFGYPVYV 0.68 0.46 I HLA-A*0201 1hhg 1i4f HLA-A*0201 9 TLTSCNTSV 0.58 0.56 I HLA-A*0201 1hhh 1i4f HLA-A*0201 10 F LPSDFFPSV 1.48 0.57 I H2-Kb 1osz 1nam H2-Kb 8 RGYLYQGL 0.85 0.47 I H2-Kb 1fo0 1nam H2-Kb 8 INFDFNTI 0.62 0.35 I H2-Kb 1g6r 1nam H2-Kb 8 SIYRYYGL 0.66 0.11 I H2-Kb 1kbg 1nam H2-Kb 8 RGYVYXGL 0.40 0.06 I H2-Kb 1g7p 1nam H2-Kb 9 SRDHSRTPM 1.41 0.82 II HLA-DRB1*0101 1fyt 2iam HLA-DRB1*0101 13 PK YVKQNTLKL AT 0.69 0.35 II HLA-DRB1*0101 1klu 2iam HLA-DRB1*0101 15 GEL IGTLNAAKV PAD 0.85 0.59 II HLA-DRB1*0101 1t5w 2iam HLA-DRB1*0101 13 AA YSDQATPLL LS 0.99 0.65 II HLA-DRB1*0101 1pyw 2iam HLA-DRB1*0101 9 FVKQNAXAL 0.40 0.32 II HLA-DRB1*0101 1sje 2iam HLA-DRB1*0101 15 PE VIPMFSALS EGAT 0.70 0.37 II HLA-DRB1*0101 1aqd 2iam HLA-DRB1*0101 14 GSD WRFLRGYHQ YA 1.68 1.01 Cα RMSD values are calculated only for the nonamer binding core (shown in bold) for peptides with more than 9 residues in the X-ray crystal structures.

Publication Year: 2010


TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires.

(2011) PLoS One 6

PubMed: 22053188 | PubMedCentral: PMC3203878 | DOI: 10.1371/journal.pone.0026301

Structural superposition of predicted loops (cyan ribbon) for 1nam CDR1α (A) and 2bnr CDR3β (B) with their respective crystal references (purple ribbon).

Publication Year: 2011


T-cell receptors binding orientation over peptide/MHC class I is driven by long-range interactions.

(2012) PLoS One 7

PubMed: 23251658 | PubMedCentral: PMC3522592 | DOI: 10.1371/journal.pone.0051943

pdb name resolution [Å] TCR pMHC primaryminimum [°] secondary minimum [°] polar effective energy difference [kcal/mol] 1ao7 2.6 A6 tax/HLA-A2 0 175 4 (lower primary minimum) 1b... 2 2.5 B7 tax/HLA-A2 −5 150 0.3 1fo0 2.5 BM3.3 PBM1/H2-Kb −15 115 0.8 1g6r 2.8 2C SIYR/H2-Kb −10 145 2.2 1kj2 2.7 KB5-C20 PKB1/H2-Kb −25 − 170 1 1lp9 2 mAH312.2 P1049/HLA-A2 −5 170 3.4 1mi5 2.5 LC13 EBV/HLA-B8 10 − 170 3.2 1nam 2.7 BM3.3 RGYVYQGL/H2-Kb −15 180 2.5 1oga 1.4 JM22 FLU/HLA-A2 −5 − 120 0.1 2bnr 1.9 1G4 NY-ESO-1/HLA-A2 0 − 160 1.2 2ckb 3.2 2C dEV8/H2-Kb 0 135 1.4 2e7l 2.5 M6 QLSPFPFDL/H2-LD 25 160 1 2esv 2.6 kk50.4 CMV gpUL40/HLA-E1 −10 165 3.6 2nx5 2.7 ELS4 EPLP/HLA-B35 −15 − 160 0 2oi9 2.35 2C QL9/H2-Kbm3 20 160 1 2ol3 * 2.9 BM3.3 PBM8/H2-Kb 65 115 −0.1 3dxa 3.5 DM1 EBV/HLA-B44 0 125 3.5 3e2h 3.8 844.1 QL9/H2-Ld 20 155 2.2 3e3q 2.95 M13 QL9/H2-Ld 25 165 0.2 3ffc 2.8 CF34 EBV/HLA-B8 5 − 170 2.1 3gsn 2.8 RA14 HCMVpp65/HLA-A2 −45 − 175 −0.6 3h9s 2.7 A6 Tel1p/HLA-A2 0 − 115 6.3 3hg1 3 MEL5 MART-1/HLA-A2 0 − 170 0.7 3kpr 2.6 LC13 EEYLKAWTF/HLA-B4 5 − 155 −0.1 3kps 2.7 LC13 EEYLQAFTY/HLA-B4 5 − 160 0 3mv8 * 2.1 TK3 HPVG/HLA-B35 − 35 − 130 − 1.3 pdb name resolution [Å] TCR pMHC primary minimum [°] secondary minimum [°] effective energy difference [kcal/mol] unpublished # – A6 tax/HLA-A2 (1ao7) −5 – – 1kgc # 1.5 LC13 EBV/HLA-B8 (1mi5) −10 – – 1tcr # 2.5 2C dEV8/H2-Kb (2ckb) 15 – – 2bnu # 1.4 1G4 NY-ESO-1/HLA-A2 (2bnr) −5 150 −0.5 2nw2 # 1.4 ELS4 EPLP/HLA-B35 (2nx5) −15 − 160 1.2 2vlm # 1.98 JM22 FLU/HLA-A2 (1oga) 10 − 160 1.4 The 26 TCRpMHC crystal structures of the test set are presented as well as unbound TCR crystal structures tested against their respective pMHC.

Publication Year: 2012