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(-) Description

Title :  NITRITE COMPLEX OF TVNIR, SECOND MIDDLE DOSE DATA SET
 
Authors :  A. A. Trofimov, K. M. Polyakov, V. A. Lazarenko, A. N. Popov, T. V. Tikhon A. V. Tikhonov, V. O. Popov
Date :  07 Jun 13  (Deposition) - 11 Jun 14  (Release) - 11 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  8 Hemes C, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Trofimov, K. M. Polyakov, V. A. Lazarenko, A. N. Popov, T. V. Tikhonova, A. V. Tikhonov, V. O. Popov
Investigation Of The X-Ray-Induced Nitrite Reduction Catalysed By Cytochrome C Nitrite Reductase From The Bacterium Thioalkalivibrio Nitratireducens
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - EIGHT-HEME NITRITE REDUCTASE
    Chains: A, B
    EC Number: 1.7.2.2
    Fragment: UNP RESIDUES 33-551
    Organism Scientific: THIOALKALIVIBRIO NITRATIREDUCENS
    Organism Taxid: 1255043
    Strain: DSM 14787 / UNIQEM 213 / ALEN2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 35)

Asymmetric Unit (6, 35)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GOL5Ligand/IonGLYCEROL
3HEC16Ligand/IonHEME C
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NO26Ligand/IonNITRITE ION
6SO42Ligand/IonSULFATE ION
Biological Unit 1 (5, 93)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL15Ligand/IonGLYCEROL
3HEC48Ligand/IonHEME C
4MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NO218Ligand/IonNITRITE ION
6SO46Ligand/IonSULFATE ION

(-) Sites  (35, 35)

Asymmetric Unit (35, 35)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:113 , ALA A:114 , PRO A:116 , ASP A:125 , HIS A:126 , VAL A:129 , ARG A:131 , CYS A:184 , CYS A:187 , LYS A:188 , ARG A:242 , CYS A:299 , HIS A:300 , TYR A:303 , CYS A:305 , HIS A:361 , ASN A:486 , HEC A:603 , NO2 A:609 , HOH A:714 , HOH A:802 , HOH A:803 , HOH A:808 , HOH A:921 , HOH A:1190BINDING SITE FOR RESIDUE HEC A 601
02AC2SOFTWARECYS A:66 , HIS A:70 , GLN A:73 , LEU A:225 , CYS A:227 , CYS A:230 , HIS A:231 , ALA A:290 , MET A:384 , TYR A:395 , THR A:396 , HIS A:398 , HEC A:607 , HOH A:781 , HOH A:865 , HOH A:881 , HOH A:1166BINDING SITE FOR RESIDUE HEC A 602
03AC3SOFTWARESER A:84 , PRO A:116 , ARG A:117 , HIS A:119 , PHE A:121 , MET A:122 , ASP A:125 , CYS A:187 , CYS A:296 , CYS A:299 , HIS A:300 , HIS A:383 , MET A:384 , HEC A:601 , HEC A:604 , CA A:611 , HOH A:704 , HOH A:719 , HOH A:799BINDING SITE FOR RESIDUE HEC A 603
04AC4SOFTWAREHIS A:300 , PHE A:367 , HIS A:372 , VAL A:377 , ALA A:378 , CYS A:379 , CYS A:382 , HIS A:383 , THR A:402 , PRO A:403 , ARG A:404 , LYS A:431 , ASN A:486 , PHE A:490 , HIS A:491 , HEC A:603 , HEC A:605 , CA A:611 , GOL A:613 , HOH A:799 , HOH A:809 , HOH A:911 , HOH A:918 , HOH A:990 , HOH A:1034BINDING SITE FOR RESIDUE HEC A 604
05AC5SOFTWAREASN A:141 , TRP A:142 , GLN A:143 , HIS A:372 , PRO A:403 , ALA A:410 , CYS A:411 , CYS A:414 , HIS A:415 , TRP A:418 , ILE A:427 , HEC A:604 , HOH A:943BINDING SITE FOR RESIDUE HEC A 605
06AC6SOFTWARECYS A:14 , PHE A:15 , HIS A:18 , HIS A:25 , VAL A:33 , ASN A:34 , CYS A:35 , CYS A:38 , HIS A:39 , THR A:59 , LEU A:194 , PHE A:228 , PRO A:233 , HIS A:234 , ARG A:239 , PHE A:274 , ARG A:276 , ARG A:282 , HEC A:607 , HEC A:608 , HOH A:759 , HOH A:1193 , HOH A:1228BINDING SITE FOR RESIDUE HEC A 606
07AC7SOFTWARELYS A:29 , HIS A:30 , HIS A:37 , ALA A:65 , CYS A:66 , THR A:68 , CYS A:69 , HIS A:70 , CYS A:227 , HIS A:231 , ALA A:236 , HEC A:602 , HEC A:606 , HOH A:1181 , HOH A:1235 , HOH A:1296 , THR B:68BINDING SITE FOR RESIDUE HEC A 607
08AC8SOFTWAREGLN A:13 , CYS A:14 , CYS A:17 , HIS A:18 , HIS A:39 , HIS A:44 , VAL A:45 , ALA A:48 , SER A:49 , SER A:50 , ARG A:52 , MET A:53 , ARG A:56 , PRO A:57 , THR A:59 , LEU A:194 , ARG A:276 , GLY A:277 , HEC A:606 , HOH A:761 , HOH A:778 , HOH A:1004 , HOH A:1224 , HOH A:1229BINDING SITE FOR RESIDUE HEC A 608
09AC9SOFTWAREARG A:131 , TYR A:303 , HIS A:361 , HEC A:601 , HOH A:919 , HOH A:921 , HOH A:1190BINDING SITE FOR RESIDUE NO2 A 609
10BC1SOFTWAREGLU A:302 , TYR A:303 , LYS A:358 , GLN A:360 , HOH A:868 , HOH A:965BINDING SITE FOR RESIDUE CA A 610
11BC2SOFTWAREPRO A:116 , HEC A:603 , HEC A:604 , GOL A:613 , HOH A:911 , HOH A:928 , HOH A:1034BINDING SITE FOR RESIDUE CA A 611
12BC3SOFTWAREARG A:87 , VAL A:128 , GLN A:138 , PHE A:139 , TRP A:142 , ARG A:497 , HOH A:1109BINDING SITE FOR RESIDUE MPD A 612
13BC4SOFTWAREARG A:96 , GLU A:115 , PRO A:116 , ASN A:486 , HEC A:604 , CA A:611 , HOH A:805 , HOH A:809 , HOH A:1034 , HOH A:1038BINDING SITE FOR RESIDUE GOL A 613
14BC5SOFTWAREASP A:101 , ALA A:110 , PHE A:111 , GLN A:175 , TRP A:444 , ILE A:504 , LYS A:508 , HOH A:938 , HOH A:1192BINDING SITE FOR RESIDUE GOL A 614
15BC6SOFTWARETYR A:198 , ASN A:247 , ASP A:251 , LYS A:271 , ARG A:322 , HOH A:844BINDING SITE FOR RESIDUE GOL A 615
16BC7SOFTWARETHR A:351 , LYS A:447 , ASN A:515 , HOH A:744 , HOH A:1069 , HOH A:1183 , HOH A:1184BINDING SITE FOR RESIDUE SO4 A 616
17BC8SOFTWARESER A:212 , GLU A:213 , VAL A:214 , NO2 A:618 , HOH A:821 , HOH A:962 , HOH A:1054 , HOH A:1117BINDING SITE FOR RESIDUE NO2 A 617
18BC9SOFTWARESER A:212 , GLU A:213 , VAL A:214 , NO2 A:617 , HOH A:905 , HOH A:1054 , HOH A:1117BINDING SITE FOR RESIDUE NO2 A 618
19CC1SOFTWAREHIS B:113 , ALA B:114 , ASP B:125 , HIS B:126 , VAL B:129 , ARG B:131 , CYS B:184 , CYS B:187 , LYS B:188 , ARG B:242 , CYS B:299 , HIS B:300 , TYR B:303 , CYS B:305 , HIS B:361 , ASN B:486 , HEC B:603 , NO2 B:609 , HOH B:738 , HOH B:826 , HOH B:827 , HOH B:832 , HOH B:945 , HOH B:1217BINDING SITE FOR RESIDUE HEC B 601
20CC2SOFTWARECYS B:66 , HIS B:70 , GLN B:73 , LEU B:225 , CYS B:227 , CYS B:230 , HIS B:231 , MET B:384 , TYR B:395 , THR B:396 , HIS B:398 , HEC B:607 , HOH B:804 , HOH B:889 , HOH B:905 , HOH B:1192 , HOH B:1266BINDING SITE FOR RESIDUE HEC B 602
21CC3SOFTWARESER B:84 , PRO B:116 , ARG B:117 , HIS B:119 , PHE B:121 , MET B:122 , ASP B:125 , CYS B:187 , MET B:229 , CYS B:296 , CYS B:299 , HIS B:300 , HIS B:383 , MET B:384 , HEC B:601 , HEC B:604 , CA B:611 , HOH B:728 , HOH B:742 , HOH B:823 , HOH B:1060BINDING SITE FOR RESIDUE HEC B 603
22CC4SOFTWAREPHE B:367 , HIS B:372 , VAL B:377 , ALA B:378 , CYS B:379 , CYS B:382 , HIS B:383 , THR B:402 , PRO B:403 , ARG B:404 , LYS B:431 , ASN B:486 , PHE B:490 , HIS B:491 , HEC B:603 , HEC B:605 , CA B:611 , GOL B:613 , HOH B:823 , HOH B:833 , HOH B:935 , HOH B:942 , HOH B:1015 , HOH B:1060BINDING SITE FOR RESIDUE HEC B 604
23CC5SOFTWAREASN B:141 , TRP B:142 , GLN B:143 , VAL B:371 , HIS B:372 , PRO B:403 , ALA B:410 , CYS B:411 , CYS B:414 , HIS B:415 , TRP B:418 , ILE B:427 , HEC B:604BINDING SITE FOR RESIDUE HEC B 605
24CC6SOFTWARECYS B:14 , PHE B:15 , HIS B:18 , VAL B:33 , ASN B:34 , CYS B:35 , CYS B:38 , HIS B:39 , THR B:59 , LEU B:194 , PHE B:228 , PRO B:233 , HIS B:234 , ARG B:239 , PHE B:274 , ARG B:276 , ARG B:282 , HEC B:607 , HEC B:608 , HOH B:782 , HOH B:1214BINDING SITE FOR RESIDUE HEC B 606
25CC7SOFTWARETHR A:68 , LYS B:29 , HIS B:30 , HIS B:37 , ALA B:65 , CYS B:66 , THR B:68 , CYS B:69 , HIS B:70 , CYS B:227 , HIS B:231 , ALA B:236 , HEC B:602 , HEC B:606 , HOH B:707 , HOH B:1207 , HOH B:1238 , HOH B:1259 , HOH B:1274BINDING SITE FOR RESIDUE HEC B 607
26CC8SOFTWAREGLN B:13 , CYS B:14 , CYS B:17 , HIS B:18 , HIS B:39 , HIS B:44 , VAL B:45 , ALA B:48 , SER B:49 , ARG B:51 , ARG B:52 , MET B:53 , ARG B:56 , PRO B:57 , THR B:59 , LEU B:194 , GLN B:275 , ARG B:276 , HEC B:606 , HOH B:784 , HOH B:801 , HOH B:1029 , HOH B:1214 , HOH B:1257 , HOH B:1285BINDING SITE FOR RESIDUE HEC B 608
27CC9SOFTWAREARG B:131 , TYR B:303 , HIS B:361 , HEC B:601 , HOH B:832 , HOH B:943 , HOH B:1217BINDING SITE FOR RESIDUE NO2 B 609
28DC1SOFTWAREGLU B:302 , TYR B:303 , LYS B:358 , GLN B:360 , HOH B:892 , HOH B:989BINDING SITE FOR RESIDUE CA B 610
29DC2SOFTWAREPRO B:116 , HEC B:603 , HEC B:604 , GOL B:613 , HOH B:935 , HOH B:952 , HOH B:1060BINDING SITE FOR RESIDUE CA B 611
30DC3SOFTWAREARG B:87 , VAL B:128 , GLN B:138 , PHE B:139 , TRP B:142 , ARG B:497 , HOH B:1135BINDING SITE FOR RESIDUE MPD B 612
31DC4SOFTWAREARG B:96 , GLU B:115 , PRO B:116 , ASN B:486 , HEC B:604 , CA B:611 , HOH B:829 , HOH B:833 , HOH B:1060 , HOH B:1064BINDING SITE FOR RESIDUE GOL B 613
32DC5SOFTWAREASP B:101 , ALA B:110 , GLN B:175 , TRP B:444 , ILE B:504 , LYS B:508 , HOH B:962 , HOH B:1221BINDING SITE FOR RESIDUE GOL B 614
33DC6SOFTWARETHR B:351 , LYS B:447 , ASN B:515 , HOH B:767 , HOH B:1095 , HOH B:1210 , HOH B:1291BINDING SITE FOR RESIDUE SO4 B 615
34DC7SOFTWAREGLN B:169 , GLU B:213 , VAL B:214 , NO2 B:617 , HOH B:1143 , HOH B:1227BINDING SITE FOR RESIDUE NO2 B 616
35DC8SOFTWARESER B:212 , GLU B:213 , VAL B:214 , NO2 B:616 , HOH B:845 , HOH B:986 , HOH B:1080 , HOH B:1143BINDING SITE FOR RESIDUE NO2 B 617

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L3Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4L3Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L3Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L3Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4L3Z)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:520
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh.hhhhhhhhh.......hhhh.eehhhhhhhh.........ee...hhhhhh.hhhhhhhhhh...................hhhhhhh.hhhhhh.....hhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhhheee.....................hhhhhh........hhhhh...........hhhhhhhh.....hhhhh........ee.hhhhhhhhh.........hhhhhhhh.eeeeeeee..eeeeeeeee...hhhhhhh.....eee..ee......ee...hhh.eee...hhhhhhhhhhhhh...ee......ee.....hhhhhhh.hhhhhh..hhhhhhh.................hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l3z A   5 NLKPVDAMQCFDCHTQIEDMHTVGKHATVNCVHCHDATEHVETASSRRMGERPVTRMDLEACATCHTAQFNSFVEVRHESHPRLEKATPTSRSPMFDKLIAGHGFAFEHAEPRSHAFMLVDHFVVDRAYGGRFQFKNWQKVTDGMGAVRGAWTVLTDADPESSDQRRFLSQTATAANPVCLNCKTQDHILDWAYMGDEHEAAKWSRTSEVVEFARDLNHPLNCFMCHDPHSAGPRVVRDGLINAVVDRGLGTYPHDPVKSEQQGMTKVTFQRGREDFRAIGLLDTADSNVMCAQCHVEYNCNPGYQLSDGSRVGMDDRRANHFFWANVFDYKEAAQEIDFFDFRHATTGAALPKLQHPEAETFWGSVHERNGVACADCHMPKVQLENGKVYTSHSQRTPRDMMGQACLNCHAEWTEDQALYAIDYIKNYTHGKIVKSEYWLAKMIDLFPVAKRAGVSEDVLNQARELHYDAHLYWEWWTAENSVGFHNPDQARESLMTSISKSKEAVSLLNDAIDAQVAV 524
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524


Chain B from PDB  Type:PROTEIN  Length:520
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh.......hhhh.eehhhhhhhh.........ee...hhhhhh.hhhhhhhhhh...................hhhhhhh.hhhhhh.....hhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhhheee...................hhhhhhhh........hhhhh...........hhhhhhhh.....hhhhh........ee.hhhhhhhhh.........hhhhhhhh.eeeeeeee..eeeeeeeee...hhhhhhh.....ee...ee......ee...hhhhhee...hhhhhhhhhhhh....ee......ee.....hhhhhhh.hhhhhh..hhhhhhh.................hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l3z B   5 NLKPVDAMQCFDCHTQIEDMHTVGKHATVNCVHCHDATEHVETASSRRMGERPVTRMDLEACATCHTAQFNSFVEVRHESHPRLEKATPTSRSPMFDKLIAGHGFAFEHAEPRSHAFMLVDHFVVDRAYGGRFQFKNWQKVTDGMGAVRGAWTVLTDADPESSDQRRFLSQTATAANPVCLNCKTQDHILDWAYMGDEHEAAKWSRTSEVVEFARDLNHPLNCFMCHDPHSAGPRVVRDGLINAVVDRGLGTYPHDPVKSEQQGMTKVTFQRGREDFRAIGLLDTADSNVMCAQCHVEYNCNPGYQLSDGSRVGMDDRRANHFFWANVFDYKEAAQEIDFFDFRHATTGAALPKLQHPEAETFWGSVHERNGVACADCHMPKVQLENGKVYTSHSQRTPRDMMGQACLNCHAEWTEDQALYAIDYIKNYTHGKIVKSEYWLAKMIDLFPVAKRAGVSEDVLNQARELHYDAHLYWEWWTAENSVGFHNPDQARESLMTSISKSKEAVSLLNDAIDAQVAV 524
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4L3Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L3Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L3Z)

(-) Gene Ontology  (10, 10)

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  1.7.2.2
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  NIR_THIND | L0DSL2
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NIR_THIND | L0DSL2: 2ot4 2zo5 3d1i 3f29 3fo3 3gm6 3lg1 3lgq 3mmo 3owm 3rkh 3s7w 3sce 3uu9 4l38 4l3x 4l3y 4q0t 4q17 4q1o 4q4u 4q5b 4q5c

(-) Related Entries Specified in the PDB File

4l38 4l3x 4l3y