Citations in PubMed

Primary Citation PubMed: 12962633 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 5

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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Relating destabilizing regions to known functional sites in proteins.

(2007) BMC Bioinformatics 8

PubMed: 17470296 | PubMedCentral: PMC1890302 | DOI: 10.1186/1471-2105-8-141

Pdb id a Holo-pdb ids b N res c F res d ASA e F ASA f Cleft g Small 1e1a 13 4.2 272 2.1 T 1e3f 1bm7 , 1e4h , 1e5a , 1eta , 1tha 8 6.9 193 1.0 T 1gu7 1guf , 1n9g 31 8.5 1158 3.7 T 1gud 1rpj 24 8.3 976 ... .4 T 1gus 1gug , 1gun , 1guo 4 6.0 119 0.9 F 1gus h 1gug , 1gun , 1guo 14 20.9 110 0.8 F 1gxy 1og1 , 1og3 , 1og4 24 10.8 947 8.7 T 1hf8 1hfa , 1hg2 , 1hg5 4 1.5 329 1.4 F 1hhq 1hiy , 1b4s , 1b99 , 1bux 17 11.3 1006 2.8 T 1is5 1is3 , 1is4 , 1is6 22 16.4 663 3.0 T 1jcf 1jcg 34 10.1 820 5.6 F 1odl 1odi , 1odj 25 10.7 339 0.8 T 1ofn 1oi6 15 7.4 669 4.0 T 1tm2 1tjy 19 6.1 437 3.2 T 1upq 1upr 12 11.2 783 11.9 T 1usg 1usk , 1usi 15 4.3 268 1.0 T 1usl 2bes , 2bet 18 11.5 505 3.9 T 1w1h 1w1d , 1w1g 10 6.6 560 6.2 T 1w2i 1w2i 8 8.9 450 5.0 F 1w37 1w3i , 1w3n , 1w3t 12 4.1 107 0.3 T 1y2t 1y2x , 1y2w 27 19.0 1191 5.6 F Polysaccharide 1nof 12 3.1 471 3.2 T 1o88 15 4.2 472 3.5 T 1ob0 1e3z 41 8.5 1572 8.9 T 1ogb 1e6n , 1e6r , 1h0g , 1h0i , 1ogg 16 3.2 565 1.5 T 1qhz 1qi2 , 8a3h , 4a3h , 1e5j , 1qi0 14 4.6 590 5.2 T 1qjv 10 2.9 265 1.8 T 1uuq 1uz4 16 3.9 256 1.7 T 1w0n 1ux7 8 6.7 642 11.2 T 1w6z 1sf7 , 1sfb , 1sfg 20 15.5 891 13.6 T 1w9s 1w9t , 1w9w 12 9.0 376 5.9 F Peptide 1c7k 9 6.8 275 4.2 T 1e5t 1e8m , 1e8n , 1o6g , 1qfs , 1uop 18 2.5 485 1.7 T 1ea7 7 2.3 97 0.9 T 1gt9 1gtj , 1gtl 21 5.9 450 3.4 F 1kl4 1hqq , 1kl3 , 1kl5 , 1rsu 17 14.2 854 4.2 T 1oes 1g1f , 1g1g , 1g1h , 1ptt , 1ptu 16 5.7 885 6.6 T 1r29 1r2b 29 23.8 1760 13.8 F Protein 1e3f 1qab , 1rlb 15 13.0 971 5.0 F 1e6l 1bdj 10 7.9 775 11.7 F 1e6l 1a0o , 1eay , 1ffg , 1ffs , 1ffw 15 11.8 1212 18.4 T 1eao 1e50 , 1h9d 26 22.8 1819 28.2 F 1f2x 12 9.5 604 5.2 F 1gcp 1gcq 21 31.3 1405 33.2 F 1gqv 2bex 36 26.7 2246 28.9 F 1obq 1gka 22 12.2 1023 6.1 T 1sif 1cmx , 1fxt , 1nbf , 1otr , 1q5w , 1s1q , 1uzx 14 19.7 937 21.7 T 1tgr 1h59 15 28.8 1236 29.5 T 1uns 1jck 19 8.1 1620 13.5 F 1uns 1jwm 20 8.5 1386 11.6 F 1uol 1gzh , 1kzy 18 9.2 1301 13.1 F 1uq4 2aai 42 16.0 2796 21.6 F 1w53 12 14.3 770 8.8 T Nucleic acid 1e7l 8 5.1 352 2.0 T 1eao 1h9d , 1hjb 18 15.8 1375 21.3 F 1gqv 1hi3 , 1hi4 , 1hi5 9 6.7 245 3.2 T 1gv2 1h88 , 1h89 , 1mse 30 29.1 2289 30.2 T 1o7i 5 4.3 497 7.4 F 1okb 1emh , 1emj , 1q3f , 1ssp , 2ssp , 4skn 30 13.5 1539 15.0 T 1uol 1tsr , 1tup 19 9.7 1229 12.4 F 1uq4 1apg , 1br5 17 6.5 364 2.8 T 1utx 10 15.2 691 9.0 F 1vyi 10 9.0 1009 15.0 F Lipid 1obq 1h91 , 1i4u , 1s2p , 1s44 21 11.6 350 2.1 T 1qmd 14 3.8 465 2.9 F Metal 1e6l 1chn , 1ymv 7 5.5 350 5.3 T 1qmd 1kho 6 1.6 67 0.4 T Peptide-Protein 1mix 1mk7 , 1mk9 26 12.6 1526 11.9 F Small-Metal 1h1y 19 8.6 365 2.2 T 1h6l 2poo , 1h6l 16 4.5 627 4.4 T 1oid 1ho5 , 1hp1 , 1hpu 19 3.6 872 3.9 F Polysaccharide-Metal 1gkb 1bxh , 1cjp , 1c57 , 1ces , 1dq1 , 1gkb , 3cna , 3enr 19 8.0 586 1.8 F Lipid-Metal 1umv 1pob , 1umv , 1c1j 17 13.9 492 3.8 T Protein-Metal 1o6v 1o6s 49 10.6 2224 11.3 F Properties of known binding sites of the dataset proteins.

Publication Year: 2007


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.

( 1H15 , 1DLH ) whole 0.8 ( 1H15 , 1LO5 ) P1 0.73 ( 1ZGL , 1JWM ) P1 0.8 DRB5*0101-DRB1*0301 ( 1FV1 , 1A6A ) P1 0.81 Though P1 score is high, the other subpocket scores are low (less than 0.34) which is in accordance with study by Texier and co-workers [ 29 ] that reports difference between the two alleles in their peptide binding properties.

Publication Year: 2010


PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity.

(2013) BMC Bioinformatics 14

PubMed: 23409948 | PubMedCentral: PMC3598884 | DOI: 10.1186/1471-2105-14-52

Table 1 HLA class II crystal structures employed to identify SDRs Allele Peptide sequence PDB IDs DRB1*0101 AA YSDQATPLL LS 1T5X; 1T5W AG FKGEQGPKG EPG 2FSE PE VIPMFSALS EGAT 1SJE PE VIPMFSALS EG 1SJH... GEL IGILNAAKV PAD 1KLG ; 2IAM GEL IGTLNAAKV PAD 1KLU ; 2IAN GSD WRFLRGYHQ YA 1AQD PK YVKQNTLKL AT 1DLH; 1FYT; 1HXY; 1JWM; 1JWS; 1JWU; 1KG0; 1LO5; 2G9H ; 2ICW; 2OJE; 1R5I DRB1*0301 PVSK MRMATPLLM QA 1A6A DRB1*0401 AY MRADAAAGG A 2SEB PK YVKQNTLKL AT 1J8H DRB1*1501 ENPV VHFFKNIVT P 1BX2; 1YMM MDFAR VHFISALHG LGGG 2WBJ DRB3*0101 A WRSDEALPL G 2Q6W DRB3*0301 QV IILNHPGQI SA 3C5J DRB5*0101 GGV YHFVKKHVH ES 1H15 NPVVHF FKNIVTPRT PPPSQ 1FV1 VHF FKNIVTPRT PG 1ZGL DQB1*0201 LQ PFPQPELPY 1S9V DQB1*0602 MN LPSTKVSWA AVGGGGSLV 1UVQ DQB1*0302 SG EGSFQPSQE NP 2NNA LV EALYLVCGE RGG 1JK8 The binding cores of the peptide ligands are highlighted in bold.

Publication Year: 2013


An effective and effecient peptide binding prediction approach for a broad set of HLA-DR molecules based on ordered weighted averaging of binding pocket profiles.

(2013) Proteome Sci 11

PubMed: 24565049 | PubMedCentral: PMC3908610 | DOI: 10.1186/1477-5956-11-S1-S15

PDB ID DRB Allele Peptide Sequence Core 4E41 DRB1*0101 GELIGILNAAKVPAD IGILNAAKV 1A6A DRB1*0301 PVSKMRMATPLLMQA MRMATPLLM 1AQD DRB1*0101 VGSDWRFLRGYHQYA WRFLRGYHQ 1BX2 DRB1*1501 ENPVVHFFKNIVTPR VHFFKN... VT 1DLH DRB1*0101 PKYVKQNTLKLAT YVKQNTLKL 1FV1 DRB5*0101 NPVVHFFKNIVTPRTPPPSQ FKNIVTPRT 1FYT DRB1*0101 PKYVKQNTLKLAT YVKQNTLKL 1H15 DRB5*0101 GGVYHFVKKHVHES YHFVKKHVH 1HQR DRB5*0101 VHFFKNIVTPRTP FKNIVTPRT 1HXY DRB1*0101 PKYVKQNTLKLAT YVKQNTLKL 1J8H DRB1*0401 PKYVKQNTLKLAT YVKQNTLKL 1JWM DRB1*0101 PKYVKQNTLKLAT YVKQNTLKL 1JWS DRB1*0101 PKYVKQNTLKLAT YVKQNTLKL 1JWU DRB1*0101 PKYVKQNTLKLAT YVKQNTLKL 1KG0 DRB1*0101 PKYVKQNTLKLAT YVKQNTLKL 1KLG DRB1*0101 GELIGILNAAKVPAD IGILNAAKV 1KLU DRB1*0101 GELIGTLNAAKVPAD IGTLNAAKV 1LO5 DRB1*0101 PKYVKQNTLKLAT YVKQNTLKL 1PYW DRB1*0101 XFVKQNAAAL FVKQNAAAL 1R5I DRB1*0101 PKYVKQNTLKLAT YVKQNTLKL 1SJE DRB1*0101 PEVIPMFSALSEGATP VIPMFSALS 1SJH DRB1*0101 PEVIPMFSALSEG VIPMFSALS 1T5W DRB1*0101 AAYSDQATPLLLSPR YSDQATPLL 1T5X DRB1*0101 AAYSDQATPLLLSPR YSDQATPLL 1YMM DRB1*1501 ENPVVHFFKNIVTPRGGSGGGGG VHFFKNIVT 1ZGL DRB5*0101 VHFFKNIVTPRTPGG FKNIVTPRT 2FSE DRB1*0101 AGFKGEQGPKGEPG FKGEQGPKG 2G9H DRB1*0101 PKYVKQNTLKLAT YVKQNTLKL 2IAM DRB1*0101 GELIGILNAAKVPAD IGILNAAKV 2IAN DRB1*0101 GELIGTLNAAKVPAD IGTLNAAKV 2ICW DRB1*0101 PKYVKQNTLKLAT YVKQNTLKL 2IPK DRB1*0101 XPKWVKQNTLKLAT WVKQNTLKL 2OJE DRB1*0101 PKYVKQNTLKLAT YVKQNTLKL 2Q6W DRB3*0101 AWRSDEALPLGS WRSDEALPL 2SEB DRB1*0401 AYMRADAAAGGA MRADAAAGG 3C5J DRB3*0301 QVIILNHPGQISA IILNHPGQI 3L6F DRB1*0101 APPAYEKLSAEQSPP YEKLSAEQS 3PDO DRB1*0101 KPVSKMRMATPLLMQALPM MRMATPLLM 3PGD DRB1*0101 KMRMATPLLMQALPM MRMATPLLM 3S4S DRB1*0101 PKYVKQNTLKLAT YVKQNTLKL 3S5L DRB1*0101 PKYVKQNTLKLAT YVKQNTLKL Methods The proposed OWA-PSSM approach is introduced in the following subsections.

PDB ID OWA-PSSM TEPITOPE TEPITOPEpan MultiRTA NetMHCIIpan-2.0 4E41 IGILNAAKV IGILNAAKV IGILNAAKV IGILNAAKV LIGILNAAK 1A6A MRMATPLLM MRMATPLLM MRMATPLLM MRMATPLLM MRMATPLLM 1AQD WRFLRGYHQ WRFLRGYHQ WRFLRGYHQ WRFLRGYHQ WRFLRGYHQ 1BX2 VHFFKNIVT VHFFKNIVT VHFFKNIVT VHFFKNIVT VVHFFKNIV 1DLH YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL 1FV1 FKNIVTPRT FKNIVTPRT FKNIVTPRT VHFFKNIVT FFKNIVTPR 1FYT YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL 1H15 YHFVKKHVH YHFVKKHVH YHFVKKHVH YHFVKKHVH YHFVKKHVH 1HQR FKNIVTPRT FKNIVTPRT FKNIVTPRT VHFFKNIVT FFKNIVTPR 1HXY YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL 1J8H YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL 1JWM YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL 1JWS YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL 1JWU YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL 1KG0 YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL 1KLG IGILNAAKV IGILNAAKV IGILNAAKV IGILNAAKV LIGILNAAK 1KLU IGTLNAAKV IGTLNAAKV IGTLNAAKV IGTLNAAKV IGTLNAAKV 1LO5 YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL 1PYW FVKQNAAAL FVKQNAAAL FVKQNAAAL FVKQNAAAL FVKQNAAAL 1R5I YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL 1SJE VIPMFSALS VIPMFSALS VIPMFSALS VIPMFSALS VIPMFSALS 1SJH VIPMFSALS VIPMFSALS VIPMFSALS VIPMFSALS VIPMFSALS 1T5W YSDQATPLL YSDQATPLL YSDQATPLL SDQATPLLL YSDQATPLL 1T5X YSDQATPLL YSDQATPLL YSDQATPLL SDQATPLLL YSDQATPLL 1YMM VHFFKNIVT VHFFKNIVT VHFFKNIVT VHFFKNIVT VHFFKNIVT 1ZGL FKNIVTPRT FKNIVTPRT FKNIVTPRT VHFFKNIVT FFKNIVTPR 2FSE FKGEQGPKG FKGEQGPKG FKGEQGPKG FKGEQGPKG FKGEQGPKG 2G9H YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL 2IAM IGILNAAKV IGILNAAKV IGILNAAKV IGILNAAKV LIGILNAAK 2IAN IGTLNAAKV IGTLNAAKV IGTLNAAKV IGTLNAAKV IGTLNAAKV 2ICW YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL 2IPK WVKQNTLKL WVKQNTLKL WVKQNTLKL WVKQNTLKL WVKQNTLKL 2OJE YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL 2Q6W WRSDEALPL - WRSDEALPL WRSDEALPL WRSDEALPL 2SEB MRADAAAGG MRADAAAGG YMRADAAAG MRADAAAGG YMRADAAAG 3C5J IILNHPGQI - VIILNHPGQ IILNHPGQI IILNHPGQI 3L6F YEKLSAEQS YEKLSAEQS YEKLSAEQS YEKLSAEQS YEKLSAEQS 3PDO MRMATPLLM MRMATPLLM MRMATPLLM MRMATPLLM MRMATPLLM 3PGD MRMATPLLM MRMATPLLM MRMATPLLM MRMATPLLM KMRMATPLL 3S4S YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL 3S5L YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL YVKQNTLKL Correct 41/41 39/41 36/41 32/41 Correct I 39/39 39/39 38/39 34/39 30/39 Correct II 2/2 1/2 2/2 2/2 Incorrectly predicted binding cores are highlighted in bold.

Publication Year: 2013


Bacterial superantigens promote acute nasopharyngeal infection by Streptococcus pyogenes in a human MHC Class II-dependent manner.

(2014) PLoS Pathog 10

PubMed: 24875883 | PubMedCentral: PMC4038607 | DOI: 10.1371/journal.ppat.1004155

To generate this model, the structures of SpeA (PDB: 1FNU) [62] and HLA-DQ8 (PDB: 1JK8) [63] were superpositioned onto the known SEC3:HLA-DR1 complex (PDB: 1JWM) [64] , and visualized using Pymol (pym... l.sourceforge.net).

Publication Year: 2014