Citations in PubMed

Primary Citation PubMed: 10894169 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 4

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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A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach.

(2008) PLoS Comput Biol 4

PubMed: 18389056 | PubMedCentral: PMC2267221 | DOI: 10.1371/journal.pcbi.1000048

Core Peptide Chain PDB ID MHC class II type PFPQPELPY LQPFPQPELPY C 1S9V DQB1*0201 EALYLVCGE LVEALYLVCGERGG C 1JK8 DQB1*0302 LPSTKVSWA EGRDSMNLPSTKVSWAAVGGGGSLVPRGSGGGG C 1UVQ DQB1�... 02a;0602 MRMATPLLM PVSKMRMATPLLMQA C 1A6A DRB1*0301 FKGEQGPKG AGFKGEQGPKGEPG E 2FSE DRB1*0101 IGILNAAKV GELIGILNAAKVPAD C 1KLG DRB1*0101 VIPMFSALS PEVIPMFSALSEGATP C 1SJE DRB1*0101 WRFLRGYHQ GSDWRFLRGYHQYA C 1AQD DRB1*0101 YSDQATPLL AAYSDQATPLLLSPR C 1T5W DRB1*0101 YVKQNTLKL PKYVKQNTLKLAT C 2G9H DRB1*0101 MRADAAAGG AYMRADAAAGGA E 2SEB DRB1*0401 YVKQNTLKL PKYVKQNTLKLAT C 1J8H DRB1*0401 VHFFKNIVT ENPVVHFFKNIVTPR C 1BX2 DRB1*1501 FKNIVTPRT NPVVHFFKNIVTPRTPPPSQ C 1FV1 DRB5*0101 YHFVKKHVH GGVYHFVKKHVHES C 1H15 DRB5*0101 AQKAKANKA FEAQKAKANKAVDGGGG B 1LNU IA b MRMATPLLM GSHSRGLPKPPKPVSKMRMATPLLMQALPMGSGSGS C 1MUJ IA b SQAVHAAHA RGISQAVHAAHAEI B 1IAO IA d TQGVTAASS GHATQGVTAASSHE B 2IAD IA d IAPVFVLLE YEIAPVFVLLEYVT B 1ES0 IA g7 RHGLDNYRG AMKRHGLDNYRGYS P 1F3J IA g7 DYGILQINS STDYGILQINSRW P 1IAK IA k HRGAIEWEG GNSHRGAIEWEGIESG P 1D9K IA k GGASQYRPS HSRGGASQYRPSQRHGTGSGSGS P 1K2D IA u IAYLKQASA ADLIAYLKQASAKGG B 1KTD IEK IAYLKQATK ADLIAYLKQATKGGG B 1KT2 IEK IAYPKAATK ADLIAYPKAATKF E 1R5V IEK ITAFNDGLK KKVITAFNDGLKGGG B 1FNE IEK ITAFNEGLK KKVITAFNEGLKGGG B 1I3R IEK 10.1371/journal.pcbi.1000048.

Publication Year: 2008


A new model defines the minimal set of polymorphism in HLA-DQ and -DR that determines susceptibility and resistance to autoimmune diabetes.

(2008) Biol Direct 3

PubMed: 18854049 | PubMedCentral: PMC2590596 | DOI: 10.1186/1745-6150-3-42

The rare histidine at β9 in I-Ag7 is charged and constrains the reactive phenolic hydroxyl group of β37 Tyr through a strong hydrogen bond of 2.92 Å, from the crystal structure... of I-Ag7 with bound HEL peptide (PDB code 1F3J; [ 14 ]).

Publication Year: 2008


Towards universal structure-based prediction of class II MHC epitopes for diverse allotypes.

(2010) PLoS One 5

PubMed: 21187956 | PubMedCentral: PMC3004863 | DOI: 10.1371/journal.pone.0014383

Peptide-MHC complex structure Docked peptide sequence Backbone RMSD (Å) All-atom RMSD (Å) Core backbone RMSD (Å) Core all-atom RMSD (Å) Contacting peptide residue numbe... s H2-IA b (1MUJ) 1MUJ* PVSK MRMATPLLM QA 0.25 0.88 0.26 0.58 −1–10 1LNU FE AQKAKANKA VD 0.70 1.83 0.74 1.96 −1–10 H2-IA d (2IAD) 2IAD* see footnote 1IAO I SQAVHAAHA E 0.48 1.58 0.42 1.03 1–10 H2-IA g7 (1ES0) 1ES0* YE IAPVFVLLE Y 0.20 2.44 0.21 0.29 −1–10 1F3J MK RHGLDNYRG Y 0.83 1.79 0.75 1.27 −1–2,4–8,10 3CUP KK MREIIGWPG G 0.88 2.24 0.87 1.62 −1–5,7,8 H2-IA k (1IAK) 1IAK* ST DYGILQINS R 0.33 1.18 0.33 1.03 −1–2,4–10 H2-IA u (1K2D) 1K2D* SR GGASQYRPS Q 0.17 0.73 0.17 0.60 0,3–10 H2-IE k (1FNG) 1FNG* KV ITAFNEGLK 0.44 1.34 0.33 1.24 −1–6,8,9 1FNE KV ITAFNDGLK 0.51 1.29 0.45 1.20 0–4,6–9 1IEB RM VNHFIAEFK 0.83 1.67 0.83 1.70 0–4,6–9 1R5V DL IAYPKAATK F 0.91 2.27 0.77 0.99 −1–7,9,10 1KT2 DL IAYLKQATK 0.72 1.38 0.65 1.17 −1–4,6–9 1R5W DL IAYFKAATK F 1.43 2.42 0.93 1.20 −1–7,9,10 1KTD DL IAYLKQASA K 1.50 3.06 0.61 1.14 −1–10 Self-docking median RMSDs 0.25 1.18 0.26 0.60 Cross-docking median RMSDs 0.83 1.81 0.75 1.20 See the Table 1 caption for details.

Publication Year: 2010


An automated framework for understanding structural variations in the binding grooves of MHC class II molecules.

(2010) BMC Bioinformatics 11 Suppl 1

PubMed: 20122230 | PubMedCentral: PMC3009528 | DOI: 10.1186/1471-2105-11-S1-S55

Alleles Supertype [ 21 ] #PDB PDB Identifiers #Mol DQA1*0102-DQB1*0602 DQ1 1 1UVQ 1 DQA1*0301/2/3-DQB1*0302 DQ8 2 1JK8 , 2NNA 2 DQA1*0501/3/5/6/7/8/9-DQB1*0201/2 DQ2 1 1S9V 2 DRA*0101/2-DRB1*0101 DR1 ... 2 1AQD , 1DLH , 1FYT , 1HXY , 1JWM , 1JWS , 1JWU , 1KG0 , 1KLG , 1KLU , 1LO5 , 1PYW , 1SEB , 1SJE , 1SJH , 1T5W , 1T5X , 2FSE , 2G9H , 2IAM , 2IAN , 2IPK 32 DRA*0101/2-DRB1*0301 DR3 1 1A6A 1 DRA*0101/2-DRB1*0401 DR4 2 1J8H , 2SEB 2 DRA*0101/2-DRB1*1501 DR2 3 1BX2 , 1YMM , 2WBJ 5 DRA*0101/2-DRB3*0101 DR52 1 2Q6W 2 DRA*0101/2-DRB3*0301 DR52 1 3C5J 1 DRA*0101/2-DRB5*0101 DR51 4 1FV1 , 1H15 , 1HQR , 1ZGL 8 H2-Aa -- 1 1ES0 1 H2-Aa, H2-Ab1 -- 17 1D9K , 1F3J , 1IAK , 1IAO , 1JL4 , 1K2D , 1LNU , 1MUJ , 1U3H , 2IAD , 2P24 , 2PXY , 2Z31 , 3C5Z , 3C60 , 3C6L , 3CUP 26 H2-Ea -- 2 1IEB , 1KTD 4 H2-Ea, H2-Eb1 -- 7 1FNE , 1FNG , 1I3R , 1IEA , 1KT2 , 1R5V , 1R5W 16 Some MHC molecules of the same type are in different branches of the cladogram calculated for the whole groove, however clustering at the sub-pocket level was more in line with the different MHC molecule types, particularly for the P4 sub-pocket.

Publication Year: 2010