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PDB ID Mentions in PubMed Central Article count: 6

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PDB ID Mentions in PubMed Central

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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


Structural deformation upon protein-protein interaction: a structural alphabet approach.

(2008) BMC Struct Biol 8

PubMed: 18307769 | PubMedCentral: PMC2315654 | DOI: 10.1186/1472-6807-8-12

We consider the 3 classes from Table 3 , namely enzyme/substrate, antibody/antigen, and other; Table 3 Description of the complex set Type (number) Complexes PDB id Enzyme-substrate (23) 1ACB , 1AVX ,... 1AY7 , 1BVN , 1CGI , 1D6R , 1DFJ , 1E6E , 1EAW , 1EWY , 1EZU , 1F34 , 1HIA , 1KKL , 1MAH , 1PPE , 1TMQ , 1UDI , 2MTA , 2PCC , 2SIC , 2SNI , 7CEI Antibody-Antigen (10) 1AHW , 1BGX , 1BVK , 1DQJ , 1E6J , 1JPS , 1MLC , 1VFB , 1WEJ , 2VIS Other (35) 1A2K , 1AK4 , 1AKJ , 1ATN , 1B6C , 1BUH , 1DE4 , 1E96 , 1EER , 1F51 , 1FC2 , 1FQ1 , 1FQJ , 1GCQ , 1GP2 , 1GRN , 1H1V , 1HE1 , 1HE8 , 1I2M , 1I4D , 1IB1 , 1IBR , 1IJK , 1KLU , 1KTZ , 1KXP , 1M10 , 1ML0 , 1N2C , 1QA9 , 1RLB , 1SBB , 1WQ1 , 2BTF • the motif should be located in totality at the protein-protein interfaces of the complexes; • we do not consider runs of helical letters (A,a,V,W,Z,B,C) or extended letters (L,M,N,T,X,J,K).

Publication Year: 2008


Protein-protein docking using region-based 3D Zernike descriptors.

(2009) BMC Bioinformatics 10

PubMed: 20003235 | PubMedCentral: PMC2800122 | DOI: 10.1186/1471-2105-10-407

Original ZDOCK Rank Context Shapes (CS) PatchDock ZDOCK Decoys Reranked by LZerD Score LZerD Complex Rank a) iRMSD HIT2K Rank iRMSD RMSD iRMSD Rank iRMSD HIT2K Rank iRMSD HIT2K 1AHW 268 2.28 21 402 2.... 6 181 2.49 15 1.68 50 5 1.34 42 1AK4 - b) - - - - - - (NA NA NA) 43787 2.35 0 1AKJ 4872 2.29 0 - - - - 1985 1.93 1 - - - 1AVX 2863 2.23 0 - - - - 5689 2.22 0 786 2.41 2 1AY7 5584 1.33 0 - - - - 394 1.1 7 1884 1.98 1 1B6C 1717 2.43 2 - - - - 497 2.13 8 1001 2.41 1 1BJ1 129 0.86 49 1893 1.93 - - 306 1.01 20 298 1.86 7 1BUH 14556 2.37 0 - - - - 11230 2.42 0 12251 1.6 0 1BVK 3970 1.94 0 - - 2754 2.27 9560 2.43 0 5515 2.24 0 1BVN 502 1.97 13 34 2.34 - - 8 2.26 59 27 2.32 6 1CGI 145 2.44 9 - - 1120 2.11 1775 2.14 1 9041 2.1 0 1D6R 2951 2.03 0 - - - - 5022 2.49 0 2619 2.24 0 1DFJ 9 2.27 40 - - - - 9350 2.14 0 - - - 1DQJ 2287 2.48 0 - - - - 5391 2.32 0 20816 2.09 0 1E6E 22643 2.08 0 - - - - 432 1.94 2 52 2.13 8 1E6J 15 1.56 34 - - - - 2509 1.81 0 439 2.18 8 1E96 3094 2.26 0 - - - - 882 1.88 2 216 2.14 2 1EAW 3 1.54 62 94 2.29 85 2.29 5 1.48 111 20 2.42 10 1EWY 259 2.32 2 - - - - 1007 2.14 4 349 2.36 14 1EZU 1100 1.94 3 - - - - 589 1.42 4 824 1.21 2 1F34 5 2.2 13 - - 490 1.81 5082 1.61 0 - - - 1F51 230 2.18 4 - - - - 154 1.76 5 3545 1.58 0 1FQJ 9889 2.29 0 - - - - 628 2.39 2 - - - 1FSK 1 1.63 105 20 1.57 221 2.39 29 1.57 76 15 2.4 11 1GCQ 24339 2.29 0 - - - - 39221 2.29 0 9418 1.8 0 1GHQ - - - - - - - (NA NA NA) 15357 1.68 0 1GRN 1704 2.34 2 - - - - 1884 1.74 1 1407 2.18 1 1HE1 4672 1.31 0 1029 2.17 - - 51 2 8 267 1.98 2 1HIA - - - - - - - (NA NA NA) 44189 2.42 0 1I9R 50 2.45 41 - - - - 57 1.96 10 95 2.39 21 1IJK 52731 2.44 0 - - - - 39460 2.44 0 6731 2.45 0 1IQD 612 2.27 5 - - - - 36 0.99 27 41 1.2 18 1JPS 171 1.81 9 - - - - 5305 1.37 0 292 0.9 20 1K4C 20806 1.53 0 - - - - 4468 1.18 0 1188 1.43 7 1KAC 2896 2.33 0 - - - - 1313 2.33 1 655 2.18 3 1KTZ 53599 1.69 0 - - - - 33926 1.69 0 12162 1.19 0 1KXP 1734 2.36 1 - - - - 32023 1.91 0 14208 2.22 0 1KXQ 212 1.91 13 2226 1.73 - - 629 1.24 4 73 1.68 14 1MAH 92 1.31 9 597 1.16 887 2.28 541 0.89 6 92 0.87 2 1ML0 36 1.56 21 - - 231 2.02 406 1.37 6 559 2.38 3 1MLC 110 1.19 12 18 2.28 - - 243 1.07 12 1834 1.16 1 1NCA 14 1.93 47 - - - - 302 1.55 12 12528 1.5 0 1NSN 185 1.81 5 26 1.79 - - 147 1.81 13 945 2.29 1 1PPE 1 0.57 218 2 2.31 - - 1 0.72 194 1 0.83 68 1QA9 5672 1.88 0 - - - - 5924 1.82 0 1381 2.19 3 1QFW 257 1.14 7 597 1.73 - - 136 2.31 17 108 1.24 4 1RLB - - - - - - - (NA NA NA) 46073 1.24 0 1TMQ 314 1.88 11 783 1.68 1 1.96 90 1.45 19 50 1.45 5 1UDI 258 2.17 4 2649 2.14 27 2.42 219 2.39 3 59 2.36 6 1VFB 2734 1.79 0 228 2.46 - - 1534 1.61 1 1303 1.69 1 1WEJ 465 2.37 8 - - - - 916 1.97 1 3914 2.06 6 1WQ1 1101 2.49 2 - - - - 284 2.05 2 141 1.87 2 2JEL 45 1.79 33 - - - - 149 2.44 19 133 2.49 9 2MTA - - - - - 515 2.19 (NA NA NA) 606 1.64 11 2PCC - - - - - - - (NA NA NA) 4542 2.31 0 2QFW 832 2.29 3 33 2.32 - - 42 1.99 17 68 1.55 29 2SIC 173 1.86 24 1077 2.28 - - 17 1.85 61 12 2.04 9 2SNI 17906 2.44 0 - - - - 428 2.33 2 - - - 7CEI 106 1.97 24 2290 1.9 366 1.07 705 1.57 7 6765 2.03 0 Summary c) ZDOCK CS PatchDock (PD) LZerD Rerank LZerD Rank<100 11 7 3 11 14 Rank<500 26 9 6 26 23 Rank<1000 29 12 9 32 29 Rank<2000 33 15 10 38 36 Wins vs. LZerD Rerank ZDOCK/LZerD Rerank 26/26 CS/LZerD Rerank 5/34 PD/LZerD Rerank 7/34 - - Wins vs. LZerD ZDOCK/LZerD 24/33 CS/LZerD 5/34 PD/LZerD 8/34 LZerD Rerank/LZerD 24/28 - LZerD results are compared with ZDOCK, Context Shapes, and PatchDock.

Publication Year: 2009


Designing coarse grained-and atom based-potentials for protein-protein docking.

(2010) BMC Struct Biol 10

PubMed: 21078143 | PubMedCentral: PMC2996388 | DOI: 10.1186/1472-6807-10-40

Table 5 Ranking ZDOCK2.3 decoys (IRMSD ≤2.5Å) by the jackknife test Complex Rank a ADPs-II b Zdock2.3 1B6C 311 168 1BVK - - 1DQJ - - 1EWY 754 113 1IJK 1131 - 1AVX 955 449 1D6R - - 1E96... 326 399 1F34 - 26 1GCQ - - 1GRN 492 807 1KXP 381 7 1NSN - 445 1SBB - - 1AKJ - 96 1AY7 236 - 1DFJ 720 1 1EAW 152 13 1I9R 329 90 1UDI 386 13 2PCC - - 1AHW 23 56 1BUH 16 - 1E6E 2 103 1ML0 10 1 1PPE 3 1 1QFW 1080 74 1TMQ 9 126 1WEJ 3 102 2JEL 307 86 7CEI 42 1 1BJ1 6 18 1CGI - - 1F51 1 11 1KAC - 1523 1NCA 4 4 1QA9 - - 2SNI 17 - 1RLB 48 302 Top10 8 (20.5%) 6 (15.4%) a-Rank of the lowest energy near-native decoy with IRMSD ≤2.5Å out of 54000 predictions.

Table 4 Ranking ZDOCK2.3 decoys (IRMSD ≤4Å) by the jackknife test Complex a Rank b ADPs-II c Zdock2.3 DARS ACE 1AK4 - - 950 1744 1B6C 95 16 9 178 1BVK 12 268 610 - 1DQJ - 1490 - - 1EWY 164 18 42 364 1FC2 484 - 24 797 1GHQ - - - 1308 1HIA 21 653 122 - 1IJK 1131 - 368 - 1KLU - - - - 1AVX 5 46 6 59 1D6R 1840 567 - - 1E96 39 399 42 490 1F34 13 26 666 5 1GCQ 1030 - 1057 1040 1GRN 210 102 - - 1I4D 84 403 965 616 1KXP 91 7 1 200 1NSN 53 445 - - 1SBB - - - - 1ACB 113 55 24 98 1AKJ 592 40 - - 1AY7 120 100 - - 1DFJ 37 1 - - 1EAW 65 13 33 309 1FQ1 - - - - 1GP2 4 389 58 1681 1I9R 184 14 589 - 1UDI 27 13 1 1 2PCC 203 193 821 120 1AHW 23 14 - - 1BUH 14 - 555 - 1E6E 2 103 44 520 1ML0 10 1 9 32 1PPE 3 1 1 1 1QFW 544 74 - - 1TMQ 9 126 12 22 1WEJ 3 42 1047 - 2JEL 307 86 76 579 7CEI 15 1 920 708 1ATN - - - - 1BJ1 6 18 18 85 1CGI 71 247 13 24 1F51 1 11 251 797 1KAC 121 1389 - - 1KKL 283 - 1 222 1NCA 4 4 - - 1QA9 687 - - - 2SNI 17 618 1 2 1RLB 48 302 5 7 a-Complex PDB code.

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

without ligand with ligand PDB ligand N 5 µ (N 5 ) [σ(N 5 )] P success I rmsd (Å) N 5 µ (N 5 ) [σ(N 5 )] P success I rmsd (Å) 1EWY FAD 1 1.0 [1.1] 0.02 ... .01 3 2.6 [1.2] 0.22 1.07 1GRN GDP, Mg 1 1.1 [1.0] 0.02 1.24 2 2.3 [1.2] 0.18 1.02 1WQ1 GDP, Mg 3 2.8 [1.3] 0.30 1.48 2 1.9 [1.2] 0.12 2.90 1RLB Retinoic acid 1 0.8 [0.9] 0.01 3.88 2 2.1 [1.3] 0.16 1.99 1R8S GDP 0 0.0 [0.0] 0.00 5.21 0 0.0 [0.0] 0.0 4.19 Discussion In this study we benchmarked the docking performance of the new RosettaDock v3.2 against the diverse Protein Docking Benchmark 3.0, marking the most comprehensive benchmarking of the RosettaDock algorithm.

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


Deciphering the shape and deformation of secondary structures through local conformation analysis.

(2011) BMC Struct Biol 11

PubMed: 21284872 | PubMedCentral: PMC3224362 | DOI: 10.1186/1472-6807-11-9

The second example shows the deformation of residues 100-103, forming a loop at the surface of the transthyretin upon complexation with a molecule of retinol-binding protein ([PDB: 1RLB ] chain A).

Publication Year: 2011