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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF THE THROMBIN-THROMBOMODULIN COMPLEX
Keywords SERINE PROTEINASE, EGF-LIKE DOMAINS, ANTICOAGULANT COMPLEX, ANTIFIBRINOLYTIC COMPLEX, HYDROLASE-HYDROLASE INHIBITOR COM
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   1DX5     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   THROMBIN LIGHT CHAIN  A 36 287 0
2  Protein   THROMBIN LIGHT CHAIN  B 36 287 0
3  Protein   THROMBIN LIGHT CHAIN  C 36 287 0
4  Protein   THROMBIN LIGHT CHAIN  D 36 287 0
5  Protein   THROMBOMODULIN  I 118 874 0
6  Protein   THROMBOMODULIN  J 118 874 0
7  Protein   THROMBOMODULIN  K 118 874 0
8  Protein   THROMBOMODULIN  L 118 874 0
9  Protein   THROMBIN HEAVY CHAIN  M 259 2094 0
10  Protein   THROMBIN HEAVY CHAIN  N 259 2094 0
11  Protein   THROMBIN HEAVY CHAIN  O 259 2094 0
12  Protein   THROMBIN HEAVY CHAIN  P 259 2094 0
13  Ligand   THROMBOMODULIN  I 3 0 5
14  Ligand   THROMBOMODULIN  J 3 0 5
15  Ligand   THROMBOMODULIN  K 3 0 5
16  Ligand   THROMBOMODULIN  L 3 0 5
17  Ligand   THROMBIN HEAVY CHAIN  M 6 0 40
18  Ligand   THROMBIN HEAVY CHAIN  N 6 0 40
19  Ligand   THROMBIN HEAVY CHAIN  O 6 0 40
20  Ligand   THROMBIN HEAVY CHAIN  P 7 0 43
21 Water     815 0 815
total       2504 13020 998
Proteins
Unit 1 CYS1 ASP1A ALA1B GLU1C GLY1D SER1E GLY1F PHE1G THR1H GLY2 LEU3 ARG4 PRO5 LEU6 PHE7 GLU8 LYS9 LYS10 SER11 LEU12 GLU13 ASP14 LYS14A THR14B GLU14C ARG14D GLU14E LEU14F LEU14G GLU14H SER14I TYR14J ILE14K ASP14L GLY14M ARG15
Unit 2 CYS1 ASP1A ALA1B GLU1C GLY1D SER1E GLY1F PHE1G THR1H GLY2 LEU3 ARG4 PRO5 LEU6 PHE7 GLU8 LYS9 LYS10 SER11 LEU12 GLU13 ASP14 LYS14A THR14B GLU14C ARG14D GLU14E LEU14F LEU14G GLU14H SER14I TYR14J ILE14K ASP14L GLY14M ARG15
Unit 3 CYS1 ASP1A ALA1B GLU1C GLY1D SER1E GLY1F PHE1G THR1H GLY2 LEU3 ARG4 PRO5 LEU6 PHE7 GLU8 LYS9 LYS10 SER11 LEU12 GLU13 ASP14 LYS14A THR14B GLU14C ARG14D GLU14E LEU14F LEU14G GLU14H SER14I TYR14J ILE14K ASP14L GLY14M ARG15
Unit 4 CYS1 ASP1A ALA1B GLU1C GLY1D SER1E GLY1F PHE1G THR1H GLY2 LEU3 ARG4 PRO5 LEU6 PHE7 GLU8 LYS9 LYS10 SER11 LEU12 GLU13 ASP14 LYS14A THR14B GLU14C ARG14D GLU14E LEU14F LEU14G GLU14H SER14I TYR14J ILE14K ASP14L GLY14M ARG15
Unit 5 VAL345 GLU346 PRO347 VAL348 ASP349 PRO350 CYS351 PHE352 ARG353 ALA354 ASN355 CYS356 GLU357 TYR358 GLN359 CYS360 GLN361 PRO362 LEU363 ASP364 GLN365 THR366 SER367 TYR368 LEU369 CYS370 VAL371 CYS372 ALA373 GLU374 GLY375 PHE376 ALA377 PRO378 ILE379 PRO380 HIS381 GLU382 PRO383 HIS384 ARG385 CYS386 GLN387 MET388 PHE389 CYS390 ASN391 GLN392 THR393 ALA394 CYS395 PRO396 ALA397 ASP398 CYS399 ASP400 PRO401 ASN402 THR403 GLN404 ALA405 SER406 CYS407 GLU408 CYS409 PRO410 GLU411 GLY412 TYR413 ILE414 LEU415 ASP416 ASP417 GLY418 PHE419 ILE420 CYS421 THR422 ASP423 ILE424 ASP425 GLU426 CYS427 GLU428 ASN429 GLY430 GLY431 PHE432 CYS433 SER434 GLY435 VAL436 CYS437 HIS438 ASN439 LEU440 PRO441 GLY442 THR443 PHE444 GLU445 CYS446 ILE447 CYS448 GLY449 PRO450 ASP451 SER452 ALA453 LEU454 ALA455 GLY456 GLN457 ILE458 GLY459 THR460 ASP461 CYS462
Unit 6 VAL345 GLU346 PRO347 VAL348 ASP349 PRO350 CYS351 PHE352 ARG353 ALA354 ASN355 CYS356 GLU357 TYR358 GLN359 CYS360 GLN361 PRO362 LEU363 ASP364 GLN365 THR366 SER367 TYR368 LEU369 CYS370 VAL371 CYS372 ALA373 GLU374 GLY375 PHE376 ALA377 PRO378 ILE379 PRO380 HIS381 GLU382 PRO383 HIS384 ARG385 CYS386 GLN387 MET388 PHE389 CYS390 ASN391 GLN392 THR393 ALA394 CYS395 PRO396 ALA397 ASP398 CYS399 ASP400 PRO401 ASN402 THR403 GLN404 ALA405 SER406 CYS407 GLU408 CYS409 PRO410 GLU411 GLY412 TYR413 ILE414 LEU415 ASP416 ASP417 GLY418 PHE419 ILE420 CYS421 THR422 ASP423 ILE424 ASP425 GLU426 CYS427 GLU428 ASN429 GLY430 GLY431 PHE432 CYS433 SER434 GLY435 VAL436 CYS437 HIS438 ASN439 LEU440 PRO441 GLY442 THR443 PHE444 GLU445 CYS446 ILE447 CYS448 GLY449 PRO450 ASP451 SER452 ALA453 LEU454 ALA455 GLY456 GLN457 ILE458 GLY459 THR460 ASP461 CYS462
Unit 7 VAL345 GLU346 PRO347 VAL348 ASP349 PRO350 CYS351 PHE352 ARG353 ALA354 ASN355 CYS356 GLU357 TYR358 GLN359 CYS360 GLN361 PRO362 LEU363 ASP364 GLN365 THR366 SER367 TYR368 LEU369 CYS370 VAL371 CYS372 ALA373 GLU374 GLY375 PHE376 ALA377 PRO378 ILE379 PRO380 HIS381 GLU382 PRO383 HIS384 ARG385 CYS386 GLN387 MET388 PHE389 CYS390 ASN391 GLN392 THR393 ALA394 CYS395 PRO396 ALA397 ASP398 CYS399 ASP400 PRO401 ASN402 THR403 GLN404 ALA405 SER406 CYS407 GLU408 CYS409 PRO410 GLU411 GLY412 TYR413 ILE414 LEU415 ASP416 ASP417 GLY418 PHE419 ILE420 CYS421 THR422 ASP423 ILE424 ASP425 GLU426 CYS427 GLU428 ASN429 GLY430 GLY431 PHE432 CYS433 SER434 GLY435 VAL436 CYS437 HIS438 ASN439 LEU440 PRO441 GLY442 THR443 PHE444 GLU445 CYS446 ILE447 CYS448 GLY449 PRO450 ASP451 SER452 ALA453 LEU454 ALA455 GLY456 GLN457 ILE458 GLY459 THR460 ASP461 CYS462
Unit 8 VAL345 GLU346 PRO347 VAL348 ASP349 PRO350 CYS351 PHE352 ARG353 ALA354 ASN355 CYS356 GLU357 TYR358 GLN359 CYS360 GLN361 PRO362 LEU363 ASP364 GLN365 THR366 SER367 TYR368 LEU369 CYS370 VAL371 CYS372 ALA373 GLU374 GLY375 PHE376 ALA377 PRO378 ILE379 PRO380 HIS381 GLU382 PRO383 HIS384 ARG385 CYS386 GLN387 MET388 PHE389 CYS390 ASN391 GLN392 THR393 ALA394 CYS395 PRO396 ALA397 ASP398 CYS399 ASP400 PRO401 ASN402 THR403 GLN404 ALA405 SER406 CYS407 GLU408 CYS409 PRO410 GLU411 GLY412 TYR413 ILE414 LEU415 ASP416 ASP417 GLY418 PHE419 ILE420 CYS421 THR422 ASP423 ILE424 ASP425 GLU426 CYS427 GLU428 ASN429 GLY430 GLY431 PHE432 CYS433 SER434 GLY435 VAL436 CYS437 HIS438 ASN439 LEU440 PRO441 GLY442 THR443 PHE444 GLU445 CYS446 ILE447 CYS448 GLY449 PRO450 ASP451 SER452 ALA453 LEU454 ALA455 GLY456 GLN457 ILE458 GLY459 THR460 ASP461 CYS462
Unit 9 ILE16 VAL17 GLU18 GLY19 SER20 ASP21 ALA22 GLU23 ILE24 GLY25 MET26 SER27 PRO28 TRP29 GLN30 VAL31 MET32 LEU33 PHE34 ARG35 LYS36 SER36A PRO37 GLN38 GLU39 LEU40 LEU41 CYS42 GLY43 ALA44 SER45 LEU46 ILE47 SER48 ASP49 ARG50 TRP51 VAL52 LEU53 THR54 ALA55 ALA56 HIS57 CYS58 LEU59 LEU60 TYR60A PRO60B PRO60C TRP60D ASP60E LYS60F ASN60G PHE60H ILE60I GLU61 ASN62 ASP63 LEU64 LEU65 VAL66 ARG67 ILE68 GLY69 LYS70 HIS71 SER72 ARG73 THR74 ARG75 TYR76 GLU77 ARG77A ASN78 ILE79 GLU80 LYS81 ILE82 SER83 MET84 LEU85 GLU86 LYS87 ILE88 TYR89 ILE90 HIS91 PRO92 ARG93 TYR94 ASN95 TRP96 ARG97 GLU97A ASN98 LEU99 ASP100 ARG101 ASP102 ILE103 ALA104 LEU105 MET106 LYS107 LEU108 LYS109 LYS110 PRO111 VAL112 ALA113 PHE114 SER115 ASP116 TYR117 ILE118 HIS119 PRO120 VAL121 CYS122 LEU123 PRO124 ASP125 ARG126 GLU127 THR128 ALA129 ALA129A SER129B LEU129C LEU130 GLN131 ALA132 GLY133 TYR134 LYS135 GLY136 ARG137 VAL138 THR139 GLY140 TRP141 GLY142 ASN143 LEU144 LYS145 GLU146 THR147 TRP148 THR149 ALA149A ASN149B VAL149C GLY149D LYS149E GLY150 GLN151 PRO152 SER153 VAL154 LEU155 GLN156 VAL157 VAL158 ASN159 LEU160 PRO161 ILE162 VAL163 GLU164 ARG165 PRO166 VAL167 CYS168 LYS169 ASP170 SER171 THR172 ARG173 ILE174 ARG175 ILE176 THR177 ASP178 ASN179 MET180 PHE181 CYS182 ALA183 GLY184 TYR184A LYS185 PRO186 ASP186A GLU186B GLY186C LYS186D ARG187 GLY188 ASP189 ALA190 CYS191 GLU192 GLY193 ASP194 SER195 GLY196 GLY197 PRO198 PHE199 VAL200 MET201 LYS202 SER203 PRO204 PHE204A ASN204B ASN205 ARG206 TRP207 TYR208 GLN209 MET210 GLY211 ILE212 VAL213 SER214 TRP215 GLY216 GLU217 GLY219 CYS220 ASP221 ARG221A ASP222 GLY223 LYS224 TYR225 GLY226 PHE227 TYR228 THR229 HIS230 VAL231 PHE232 ARG233 LEU234 LYS235 LYS236 TRP237 ILE238 GLN239 LYS240 VAL241 ILE242 ASP243 GLN244 PHE245 GLY246 GLU247
Unit 10 ILE16 VAL17 GLU18 GLY19 SER20 ASP21 ALA22 GLU23 ILE24 GLY25 MET26 SER27 PRO28 TRP29 GLN30 VAL31 MET32 LEU33 PHE34 ARG35 LYS36 SER36A PRO37 GLN38 GLU39 LEU40 LEU41 CYS42 GLY43 ALA44 SER45 LEU46 ILE47 SER48 ASP49 ARG50 TRP51 VAL52 LEU53 THR54 ALA55 ALA56 HIS57 CYS58 LEU59 LEU60 TYR60A PRO60B PRO60C TRP60D ASP60E LYS60F ASN60G PHE60H ILE60I GLU61 ASN62 ASP63 LEU64 LEU65 VAL66 ARG67 ILE68 GLY69 LYS70 HIS71 SER72 ARG73 THR74 ARG75 TYR76 GLU77 ARG77A ASN78 ILE79 GLU80 LYS81 ILE82 SER83 MET84 LEU85 GLU86 LYS87 ILE88 TYR89 ILE90 HIS91 PRO92 ARG93 TYR94 ASN95 TRP96 ARG97 GLU97A ASN98 LEU99 ASP100 ARG101 ASP102 ILE103 ALA104 LEU105 MET106 LYS107 LEU108 LYS109 LYS110 PRO111 VAL112 ALA113 PHE114 SER115 ASP116 TYR117 ILE118 HIS119 PRO120 VAL121 CYS122 LEU123 PRO124 ASP125 ARG126 GLU127 THR128 ALA129 ALA129A SER129B LEU129C LEU130 GLN131 ALA132 GLY133 TYR134 LYS135 GLY136 ARG137 VAL138 THR139 GLY140 TRP141 GLY142 ASN143 LEU144 LYS145 GLU146 THR147 TRP148 THR149 ALA149A ASN149B VAL149C GLY149D LYS149E GLY150 GLN151 PRO152 SER153 VAL154 LEU155 GLN156 VAL157 VAL158 ASN159 LEU160 PRO161 ILE162 VAL163 GLU164 ARG165 PRO166 VAL167 CYS168 LYS169 ASP170 SER171 THR172 ARG173 ILE174 ARG175 ILE176 THR177 ASP178 ASN179 MET180 PHE181 CYS182 ALA183 GLY184 TYR184A LYS185 PRO186 ASP186A GLU186B GLY186C LYS186D ARG187 GLY188 ASP189 ALA190 CYS191 GLU192 GLY193 ASP194 SER195 GLY196 GLY197 PRO198 PHE199 VAL200 MET201 LYS202 SER203 PRO204 PHE204A ASN204B ASN205 ARG206 TRP207 TYR208 GLN209 MET210 GLY211 ILE212 VAL213 SER214 TRP215 GLY216 GLU217 GLY219 CYS220 ASP221 ARG221A ASP222 GLY223 LYS224 TYR225 GLY226 PHE227 TYR228 THR229 HIS230 VAL231 PHE232 ARG233 LEU234 LYS235 LYS236 TRP237 ILE238 GLN239 LYS240 VAL241 ILE242 ASP243 GLN244 PHE245 GLY246 GLU247
Unit 11 ILE16 VAL17 GLU18 GLY19 SER20 ASP21 ALA22 GLU23 ILE24 GLY25 MET26 SER27 PRO28 TRP29 GLN30 VAL31 MET32 LEU33 PHE34 ARG35 LYS36 SER36A PRO37 GLN38 GLU39 LEU40 LEU41 CYS42 GLY43 ALA44 SER45 LEU46 ILE47 SER48 ASP49 ARG50 TRP51 VAL52 LEU53 THR54 ALA55 ALA56 HIS57 CYS58 LEU59 LEU60 TYR60A PRO60B PRO60C TRP60D ASP60E LYS60F ASN60G PHE60H ILE60I GLU61 ASN62 ASP63 LEU64 LEU65 VAL66 ARG67 ILE68 GLY69 LYS70 HIS71 SER72 ARG73 THR74 ARG75 TYR76 GLU77 ARG77A ASN78 ILE79 GLU80 LYS81 ILE82 SER83 MET84 LEU85 GLU86 LYS87 ILE88 TYR89 ILE90 HIS91 PRO92 ARG93 TYR94 ASN95 TRP96 ARG97 GLU97A ASN98 LEU99 ASP100 ARG101 ASP102 ILE103 ALA104 LEU105 MET106 LYS107 LEU108 LYS109 LYS110 PRO111 VAL112 ALA113 PHE114 SER115 ASP116 TYR117 ILE118 HIS119 PRO120 VAL121 CYS122 LEU123 PRO124 ASP125 ARG126 GLU127 THR128 ALA129 ALA129A SER129B LEU129C LEU130 GLN131 ALA132 GLY133 TYR134 LYS135 GLY136 ARG137 VAL138 THR139 GLY140 TRP141 GLY142 ASN143 LEU144 LYS145 GLU146 THR147 TRP148 THR149 ALA149A ASN149B VAL149C GLY149D LYS149E GLY150 GLN151 PRO152 SER153 VAL154 LEU155 GLN156 VAL157 VAL158 ASN159 LEU160 PRO161 ILE162 VAL163 GLU164 ARG165 PRO166 VAL167 CYS168 LYS169 ASP170 SER171 THR172 ARG173 ILE174 ARG175 ILE176 THR177 ASP178 ASN179 MET180 PHE181 CYS182 ALA183 GLY184 TYR184A LYS185 PRO186 ASP186A GLU186B GLY186C LYS186D ARG187 GLY188 ASP189 ALA190 CYS191 GLU192 GLY193 ASP194 SER195 GLY196 GLY197 PRO198 PHE199 VAL200 MET201 LYS202 SER203 PRO204 PHE204A ASN204B ASN205 ARG206 TRP207 TYR208 GLN209 MET210 GLY211 ILE212 VAL213 SER214 TRP215 GLY216 GLU217 GLY219 CYS220 ASP221 ARG221A ASP222 GLY223 LYS224 TYR225 GLY226 PHE227 TYR228 THR229 HIS230 VAL231 PHE232 ARG233 LEU234 LYS235 LYS236 TRP237 ILE238 GLN239 LYS240 VAL241 ILE242 ASP243 GLN244 PHE245 GLY246 GLU247
Unit 12 ILE16 VAL17 GLU18 GLY19 SER20 ASP21 ALA22 GLU23 ILE24 GLY25 MET26 SER27 PRO28 TRP29 GLN30 VAL31 MET32 LEU33 PHE34 ARG35 LYS36 SER36A PRO37 GLN38 GLU39 LEU40 LEU41 CYS42 GLY43 ALA44 SER45 LEU46 ILE47 SER48 ASP49 ARG50 TRP51 VAL52 LEU53 THR54 ALA55 ALA56 HIS57 CYS58 LEU59 LEU60 TYR60A PRO60B PRO60C TRP60D ASP60E LYS60F ASN60G PHE60H ILE60I GLU61 ASN62 ASP63 LEU64 LEU65 VAL66 ARG67 ILE68 GLY69 LYS70 HIS71 SER72 ARG73 THR74 ARG75 TYR76 GLU77 ARG77A ASN78 ILE79 GLU80 LYS81 ILE82 SER83 MET84 LEU85 GLU86 LYS87 ILE88 TYR89 ILE90 HIS91 PRO92 ARG93 TYR94 ASN95 TRP96 ARG97 GLU97A ASN98 LEU99 ASP100 ARG101 ASP102 ILE103 ALA104 LEU105 MET106 LYS107 LEU108 LYS109 LYS110 PRO111 VAL112 ALA113 PHE114 SER115 ASP116 TYR117 ILE118 HIS119 PRO120 VAL121 CYS122 LEU123 PRO124 ASP125 ARG126 GLU127 THR128 ALA129 ALA129A SER129B LEU129C LEU130 GLN131 ALA132 GLY133 TYR134 LYS135 GLY136 ARG137 VAL138 THR139 GLY140 TRP141 GLY142 ASN143 LEU144 LYS145 GLU146 THR147 TRP148 THR149 ALA149A ASN149B VAL149C GLY149D LYS149E GLY150 GLN151 PRO152 SER153 VAL154 LEU155 GLN156 VAL157 VAL158 ASN159 LEU160 PRO161 ILE162 VAL163 GLU164 ARG165 PRO166 VAL167 CYS168 LYS169 ASP170 SER171 THR172 ARG173 ILE174 ARG175 ILE176 THR177 ASP178 ASN179 MET180 PHE181 CYS182 ALA183 GLY184 TYR184A LYS185 PRO186 ASP186A GLU186B GLY186C LYS186D ARG187 GLY188 ASP189 ALA190 CYS191 GLU192 GLY193 ASP194 SER195 GLY196 GLY197 PRO198 PHE199 VAL200 MET201 LYS202 SER203 PRO204 PHE204A ASN204B ASN205 ARG206 TRP207 TYR208 GLN209 MET210 GLY211 ILE212 VAL213 SER214 TRP215 GLY216 GLU217 GLY219 CYS220 ASP221 ARG221A ASP222 GLY223 LYS224 TYR225 GLY226 PHE227 TYR228 THR229 HIS230 VAL231 PHE232 ARG233 LEU234 LYS235 LYS236 TRP237 ILE238 GLN239 LYS240 VAL241 ILE242 ASP243 GLN244 PHE245 GLY246 GLU247
Ligands
Unit 13 FMT501 CA502 NA503
Unit 14 FMT501 CA502 NA503
Unit 15 FMT501 CA502 NA503
Unit 16 FMT501 CA502 NA503
Unit 17 NAG301 NA302 0GJ303 0GJ304 0GJ305 0GJ306
Unit 18 NAG301 NA302 0GJ303 0GJ304 0GJ305 0GJ306
Unit 19 NAG301 NA302 0GJ303 0GJ304 0GJ305 0GJ306
Unit 20 NAG301 NA302 FMT303 0GJ304 0GJ305 0GJ306 0GJ307
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany