1TGS

THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN PANCREATIC SECRETORY INHIBITOR (KAZAL TYPE) AND TRYPSINOGEN AT 1.8 ANGSTROMS RESOLUTION. STRUCTURE SOLUTION, CRYSTALLOGRAPHIC REFINEMENT AND PRELIMINARY STRUCTURAL INTERPRETATION


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PDB ID Mentions in PubMed Central Article count: 7

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PDB ID Mentions in PubMed Central

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Computational study for protein-protein docking using global optimization and empirical potentials.

(2008) Int J Mol Sci 9

PubMed: 19325720 | PubMedCentral: PMC2635596 | DOI: null

Some protein structures, for example, 1TGS, have missing atoms and/or residues, which produces a sequence discrepancy between bound and unbound protein components.

of acceptable 1A0O 4.10 0 4.16 0 3.08 1 1ACB 1.33 D 6 0.97 9 1.28 8 1AVZ 5.73 0 4.79 0 4.90 0 1BRC 5.29 0 4.04 0 5.03 0 1BRS 10.47 0 4.96 0 7.67 0 1CGI 3.46 3 2.73 5 2.94 1 1CHO 4.02 0 1.11 3 1.45 2 1CSE 3.29 2 1.27 2 1.62 3 1MEL 9.38 0 3.66 1 7.31 0 1PPE 4.07 0 3.11 6 2.40 8 1STF 4.98 0 4.95 0 4.96 0 1TAB 5.86 0 4.98 0 5.97 0 1TGS 1.64 1 5.87 0 5.24 0 1UDI 2.14 4 4.05 0 2.25 4 2KAI 5.66 0 5.28 0 5.55 0 2PTC 5.29 0 4.98 0 5.61 0 2TEC 2.63 4 2.60 1 2.37 3 4HTC 6.14 0 7.54 0 3.57 1 A complex pdb stands for the pdb ID of the native structure of the corresponding complex-complex structures B The RMSD is defined as the RMSD over C α atoms of the interface residues between a predicted structure and its native complex and the smallest RMSD is the RMSD value calculated for the most native-like conformation in the final set C The number of the acceptable native-like structures found in the final set of 500 conformations D The smallest RMSD being “acceptable” is written with bold italic types.

Publication Year: 2008


A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys.

(2007) Proteins 69

PubMed: 17623864 | PubMedCentral: PMC2673351 | DOI: 10.1002/prot.21498

Table I The Number of Top 5 Decoys with rmsd < 10 Å given by EMPIRE and the RosettaDock scoring function Pdb ID a 1CGI 1CHO 2PTC 1TGS 2SNI 2SIC 1CSE 2KAI EMPIRE b 1 5 4 5 5 5 5 5 Roset... aDock c 4 3 2 5 4 5 2 4 Pdb ID 1BRC 1ACB 1BRS 1MAH 1UGH 1DFJ 1FSS 1AVW EMPIRE 5 3 4 5 5 5 3 5 RosettaDock 1 2 4 5 5 4 5 5 Pdb ID 1PPE 1TAB 1UDI 1STF 2TEC 4 HTC 1MLC 1WEJ EMPIRE 5 5 5 5 5 5 2 2 RosettaDock 5 5 5 5 5 5 0 0 Pdb ID 1AHW 1DQJ 1BVK 1FBI 2JEL 1BQL 1JHL 1NQA EMPIRE 0 1 1 5 5 2 1 5 RosettaDock 5 2 5 3 5 5 1 5 Pdb ID 1NMB 1MEL 2VIR 1EO8 1QFU 1IAI 2PCC 1WQ1 EMPIRE 5 5 3 1 4 3 4 4 RosettaDock 5 5 4 1 5 0 3 3 Pdb ID AVZ 1MDA 1IGC 1ATN 1GLA 1SPB 2BTF 1A0Q EMPIRE 0 4 1 5 5 5 3 4 RosettaDock 0 3 2 5 1 5 4 1 Pdb ID 1BTH 1FIN 1FQ1 1GOT 1EFU 3HHR #(≥3) d #(>) EMPIRE 0 0 4 5 2 2 39 21 e RosettaDock 0 0 2 0 0 0 34 10 f a Enzyme/Inhibitor: the first 22 protein complexes (1CGI-4HTC); antibody-antigen: the next 16 protein complexes (1MLC-1IAI); the others: (2PCC to 1A0Q); and the difficult set (1BTH to 3HHR).

Publication Year: 2007


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

(2009) BMC Bioinformatics 10

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

Complex LZerD 3DZD+NORMAL NORMAL BSA EXVOL EXVOL +BSA 1A0O 704 11917 5320 848 5888 573 1AVW 41 26 31 958 7412 696 1AVZ 21 920 554 2237 332 77 1BQL 507 6604 294 10042 23281 935 1BRC 132 221 8657 4140 2... 35 1456 1BRS 1 3 1 20 14154 6 1BTH 1 1 1 18 10176 1 1CHO 1 1 1 534 98 97 1CSE 5 22 18 208 16286 182 1EO8 3791 7869 6472 12640 204 687 1FBI 202 4055 4004 7480 9164 1053 1FSS 26 4292 3904 204 4220 85 1GLA 1161 42275 39867 12647 1377 4074 1IAI 11 45 78 895 17448 25 1IGC 2946 5887 7988 6832 2292 1827 1JHL 2901 850 1413 8706 2191 1601 1MEL 125 30081 21657 533 3405 26 1QFU 17 54 57 2571 6279 115 1SPB 1 63 36 107 27227 4 1STF 2 13 8 101 2491 3 1TAB 20 31 40 271 2878 17 1TGS 1 1 1 426 837 11 1UGH 1 4 1 5 12311 1 2KAI 37 150 337 1750 775 374 2PTC 9 9 22 1781 12777 72 2TEC 2 536 514 9261 289 7184 2VIR 5243 18668 15018 3750 5063 9594 3HHR 351 16048 901 1332 8496 382 4HTC 1 1 1 1 17361 1 Summary Wins vs. LZerD a) - 3D+N/LZD 2/22 Normal/LZD 3/20 BSA/LZD 1/27 ExVol/LZD 4/25 E+B/LZD 6/20 Wins Overall b) 20 7 7 2 1 7 The training set included 29 bound-bound protein complexes taken from Benchmark datasets 0.0 and 1.0.

Publication Year: 2009


Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective.

(2010) BMC Bioinformatics 11

PubMed: 20462403 | PubMedCentral: PMC2882391 | DOI: 10.1186/1471-2105-11-244

Chain E of 1TAB , chain Z of 1TGS , chain E of 2BTC and chain E of 2PTC are identical chains.

PDB entry First Chains Second Chains 1EJA -A:B GLN192-SER195-SER214-TRP215-GLY216 CYS33-LYS34 1TAB -E:I GLN192-SER214-TRP215-GLY216-SER217 CYS24-LYS26 1TGS -Z:I GLN192-SER214-TRP215-GLY216-SER217 CYS16-LYS18 2BTC -E:I GLN192-SER214-TRP215-GLY216-SER217 CYS503-LYS505 2PTC -E:I GLN192-SER195-SER214-TRP215-GLY216 CYS14-LYS15 1BTH -H:P GLN192-SER195-SER214-TRP215-GLY216 CYS14-LYS15 We take these examples to highlight that the uniqueness of DWE bicliques matches to different interfacial properties of the three types of protein interactions in terms of polarity, hydrophobicity, the composition of residues and residue pairs in protein interfaces.

For example, 1TGS is about 'three-dimensional structure of the complex between pancreatic secretory inhibitor (kazal type) and trypsinogen', and 2BTC is about 'bovine trypsin in complex with squash seed inhibitor (cucurbita pepo trypsin inhibitor II)'.

PDB entries 1EJA :B 1TAB :I 1TGS :I 2BTC :I 2PTC :I 1BTH :P 1EJA :A A B - - - - - 1TAB :E 83 E I - - - - 1TGS :Z 83 100 Z I - - - 2BTC :E 83 100 100 E I - - 2PTC :E 83 100 100 100 E I 100 1BTH :H 37 36 36 36 36 H P The italic half is for the sequence similarity among these inhibitors, while the bold-face half is for the sequence similarity among trypsins/trypsinogen; '-' means no significant sequence alignment.

Publication Year: 2010


Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models.

(2010) BMC Bioinformatics 11

PubMed: 20718956 | PubMedCentral: PMC2931518 | DOI: 10.1186/1471-2105-11-429

PDBcode Chain Length Rg S 1HCR A 52 6.92 0.504 1TGS I 56 6.25 0.137 1TGX A 60 6.84 0.158 1ISU A 62 6.02 0.203 1BF4 A 63 6.44 0.223 1PCF A 66 8.33 0.160 1B3A A 67 7.27 0.122 1ATZ A 75 7.24 0.214 1DP7 P... 76 7.35 0.237 3HTS B 82 7.02 0.286 3EIP A 84 7.35 0.233 2BOP A 85 7.90 0.122 1LMB 4 92 7.88 0.235 1FLT Y 94 7.55 0.132 1DIF A 99 7.82 0.260 1IIB A 103 7.38 0.228 1CMB A 104 8.35 0.116 256B A 106 8.37 0.245 1EVH A 111 7.78 0.180 1DPT A 117 8.56 0.194 1FLM B 122 8.26 0.118 2BBK L 124 8.05 0.317 1NWP A 128 7.88 0.179 1BBH A 131 9.18 0.161 1AQZ A 142 8.48 0.208 1A3A D 144 8.15 0.230 1M6P A 146 8.70 0.141 2TNF A 148 9.71 0.252 1ELK A 153 8.62 0.369 1NBC A 155 8.53 0.262 1DPS D 156 9.82 0.272 1PHN A 162 10.48 0.204 1C02 A 166 9.60 0.230 1YTB A 180 11.73 0.190 1BEH B 183 8.78 0.204 1ATL A 200 9.30 0.267 1BSM A 201 10.05 0.191 1YAC B 204 9.80 0.248 6GSV B 217 10.11 0.203 1AUO A 218 9.34 0.137 1QL0 A 241 9.59 0.165 1CYD A 242 10.13 0.287 1TPH 1 245 9.87 0.169 1A28 B 249 10.39 0.300 1C90 A 265 10.30 0.142 1AQU A 281 10.73 0.177 1BF6 B 291 10.21 0.294 1FTR A 296 12.14 0.295 4PGA A 330 11.67 0.217 1CZF A 335 11.43 0.241 S is the difference between the curves resulting from the two-body model and CRYSOL in units of "experimental" standard deviations.

Publication Year: 2010


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 2 Dataset 2 contains 40 complexes 1 1A0O 1EFN 1KB5 1TOC 1AGR 1FIN 1MEL 1TX4 1BRS 1FLE 1MKW 1YCS 1BTH 1FSS 1NFD 1YDR 1CBW 1GLA 1NMB 2KAI 1CHO 1GUA 1OSP 2PTC 1CSE 1HWG 1PPF 2TRC 1DHK 1IAI 1STF 3SG... 1DVF 1IGC 1TBQ 4CPA 1EBP 1JHL 1TGS 4HTC 1.

Publication Year: 2010


Natural and synthetic inhibitors of kallikrein-related peptidases (KLKs).

(2010) Biochimie 92

PubMed: 20615447 | PubMedCentral: PMC3014083 | DOI: 10.1016/j.biochi.2010.06.022

 5 Kazal-type inhibitor with reactive center loop (RCL) bound to the active site of a serine protease represented as molecular surface (trypsinogen with pancreatic secretory inhibitor, PDB cod... 1TGS).

Publication Year: 2010