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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN O-GLCNAC TRANSFERASE WITH UDP-5SGLCNAC AND A PEPTIDE SUBSTRATE
 
Authors :  M. B. Lazarus, J. Jiang, T. M. Gloster, W. F. Zandberg, D. J. Vocadlo, S. W
Date :  05 Sep 12  (Deposition) - 31 Oct 12  (Release) - 12 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B  (2x)
Biol. Unit 4:  C,D  (2x)
Keywords :  Ogt, O-Glcnac, Gt-B, Glycosyltransferase, Glcnacylation, Transferase- Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. B. Lazarus, J. Jiang, T. M. Gloster, W. F. Zandberg, G. E. Whitworth, D. J. Vocadlo, S. Walker
Structural Snapshots Of The Reaction Coordinate For O-Glcna Transferase.
Nat. Chem. Biol. V. 8 966 2012
PubMed-ID: 23103939  |  Reference-DOI: 10.1038/NCHEMBIO.1109

(-) Compounds

Molecule 1 - UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N- ACETYLGLUCOSAMINYLTRANSFERASE 110 KDA SUBUNIT
    ChainsA, C
    EC Number2.4.1.255
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneOGT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymO-GLCNAC TRANSFERASE SUBUNIT P110, O-LINKED N- ACETYLGLUCOSAMINE TRANSFERASE 110 KDA SUBUNIT, OGT
 
Molecule 2 - CASEIN KINASE II SUBUNIT ALPHA
    ChainsB, D
    EC Number2.7.11.1
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsSYNTHETIC PEPTIDE
    SynonymCK II ALPHA
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD
Biological Unit 3 (2x)AB  
Biological Unit 4 (2x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
112V2Ligand/Ion(2S,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-THIOPYRAN-2-YL [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGENDIPHOSPHATE
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
112V1Ligand/Ion(2S,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-THIOPYRAN-2-YL [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGENDIPHOSPHATE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
112V1Ligand/Ion(2S,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-THIOPYRAN-2-YL [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGENDIPHOSPHATE
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
112V2Ligand/Ion(2S,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-THIOPYRAN-2-YL [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGENDIPHOSPHATE
2SO44Ligand/IonSULFATE ION
Biological Unit 4 (2, 4)
No.NameCountTypeFull Name
112V2Ligand/Ion(2S,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-THIOPYRAN-2-YL [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGENDIPHOSPHATE
2SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:498 , PRO A:559 , THR A:560 , LEU A:563 , LEU A:653 , GLY A:654 , PRO A:656 , PHE A:694 , GLN A:839 , TYR A:841 , LYS A:842 , LEU A:866 , VAL A:895 , ALA A:896 , LYS A:898 , HIS A:901 , ARG A:904 , CYS A:917 , HIS A:920 , THR A:921 , THR A:922 , ASP A:925 , HOH A:1604 , HOH A:1627 , HOH A:1717 , HOH A:1765 , HOH A:1786 , THR B:18 , PRO B:19 , VAL B:20 , SER B:21 , HOH B:201BINDING SITE FOR RESIDUE 12V A 1501
2AC2SOFTWAREGLY A:365 , LEU A:367 , GLN A:368 , HOH A:1769 , HOH A:1977BINDING SITE FOR RESIDUE SO4 A 1502
3AC3SOFTWARELYS A:634 , GLY A:635 , HOH A:1798 , ASN B:24 , MET B:25BINDING SITE FOR RESIDUE SO4 B 101
4AC4SOFTWAREHIS C:498 , PRO C:559 , THR C:560 , LEU C:563 , LEU C:653 , GLY C:654 , PRO C:656 , PHE C:694 , GLN C:839 , TYR C:841 , LYS C:842 , LEU C:866 , VAL C:895 , ALA C:896 , LYS C:898 , HIS C:901 , ARG C:904 , CYS C:917 , HIS C:920 , THR C:921 , THR C:922 , ASP C:925 , HOH C:1602 , HOH C:1720 , HOH C:1789 , HOH C:1835 , THR D:18 , PRO D:19 , VAL D:20 , SER D:21 , HOH D:201 , HOH D:203BINDING SITE FOR RESIDUE 12V C 1501
5AC5SOFTWAREGLY C:635 , HOH C:1861 , ASN D:24 , MET D:25BINDING SITE FOR RESIDUE SO4 D 101
6AC6SOFTWARELEU A:371 , LYS A:375 , LEU A:395 , ASP A:400 , ASP A:431 , SER A:494 , HIS A:496 , HIS A:517 , ASN A:557 , HIS A:558 , PRO A:559 , TYR A:632 , THR A:633 , LYS A:634 , GLN A:839 , VAL A:895 , 12V A:1501 , HOH A:1620 , HOH A:1627 , TYR B:13 , SO4 B:101 , HOH B:201 , HOH B:202 , HOH B:203 , HOH B:204 , HOH B:208BINDING SITE FOR CHAIN B OF CASEIN KINASE II SUBUNIT ALPHA
7AC7SOFTWARELEU C:371 , LYS C:375 , LEU C:395 , ASP C:400 , ASP C:431 , SER C:494 , HIS C:496 , HIS C:517 , ASN C:557 , HIS C:558 , PRO C:559 , TYR C:632 , THR C:633 , LYS C:634 , GLN C:839 , VAL C:895 , 12V C:1501 , TYR D:13 , SO4 D:101 , HOH D:201 , HOH D:202 , HOH D:203 , HOH D:204 , HOH D:205 , HOH D:206 , HOH D:207 , HOH D:208 , HOH D:212 , HOH D:213BINDING SITE FOR CHAIN D OF CASEIN KINASE II SUBUNIT ALPHA

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:868 -Pro A:869
2Phe C:868 -Pro C:869

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GYY)

(-) 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:693
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh................eeeeeee.....hhhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhh.eeee.hhh.hhhhhhhhhhhh...eeee.........hhhhhh....eeeee.............eeee.....hhhhhhhh..eeee........hhhhhhhhhh..eee........eeee..hhhhhhhh....ee...eee..hhhhhhhhhhhhhh..eeee..eeeee..hhhhhhhhhhh.......eeeee.hhh......eeee...hhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhh..hhh.eeeee..hhhhhhhhhhhh.eee.......hhhhhhhhhh...ee.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gyy A  314 PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFHIYDNRIVLNGIDLKAFLDSLPDVKIVNMPVIPMNTIAEAVIEMINRGQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIK 1028
                                   323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713|      727       737      |765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025   
                                                                                                                                                                                                                                                                                                                                                                                                                                         713|                       744|                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                                          718                        763                                                                                                                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:14
                                               
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                4gyy B   13 YPGGSTPVSSANMM   26
                                    22    

Chain C from PDB  Type:PROTEIN  Length:671
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh..eeeeeee.....hhhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhh.eeee.hhh.hhhhhhhhhhhh...eeee.........hhhhhh....eeeee.............eeee.....hhhhhhhh..eeee........hhhhhhhhhh..eee........eeee..hhhhhhhh....ee...eee..hhhhhhhhhhhhhh..eeee..eeeee..hhhhhhhhhhh.......eeeee.hhh......eeee...hhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhh..hhh.eeeee..hhhhhhhhhhhh.eee.......hhhhhhhhhh...ee.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gyy C  336 AVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFHIYDNRIVLNGIDLKAFLDSLPDVKIVNMPVIPMNTIAEAVIEMINRGQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIK 1028
                                   345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       719       729       739    || 767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027 
                                                                                                                                                                                                                                                                                                                                                                                                                   713|                       744|                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                    718                        763                                                                                                                                                                                                                                                                         

Chain D from PDB  Type:PROTEIN  Length:14
                                               
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                4gyy D   13 YPGGSTPVSSANMM   26
                                    22    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 4GYY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (102, 111)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CSK21_HUMAN | P684001jwh 1na7 1pjk 2pvr 2zjw 3amy 3at2 3at3 3at4 3axw 3bqc 3c13 3fwq 3h30 3juh 3mb6 3mb7 3nga 3nsz 3owj 3owk 3owl 3pe1 3pe2 3pe4 3q04 3q9w 3q9x 3q9y 3q9z 3qa0 3r0t 3rps 3tax 3u4u 3u87 3u9c 3w8l 3war 3wik 3wil 3wow 4dgl 4fbx 4grb 4gub 4gyw 4gz3 4ib5 4kwp 4md7 4md8 4md9 4nh1 4rll 4ub7 4uba 5b0x 5clp 5cqu 5cqw 5cs6 5csh 5csp 5csv 5ct0 5ctp 5cu0 5cu2 5cu3 5cu4 5cu6 5cvf 5cvg 5cvh 5cx9 5h8b 5h8e 5h8g 5hgv 5m44 5m4c 5m4f 5m4i 5mmf 5mmr 5mo5 5mo6 5mo7 5mo8 5mod 5moe 5moh 5mot 5mov 5mow 5mp8 5mpj 5n1v 5nqc
        OGT1_HUMAN | O152941w3b 3pe3 3pe4 3tax 4ay5 4ay6 4cdr 4gyw 4gz3 4gz5 4gz6 4n39 4n3a 4n3b 4n3c 4xi9 4xif 5bnw 5c1d 5hgv 5lvv 5lwv

(-) Related Entries Specified in the PDB File

4gyw 4gz3 4gz5 4gz6