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(-) Description

Title :  CRYSTAL STRUCTURE OF HCMV PENTAMER IN COMPLEX WITH NEUTRALIZING ANTIBODY 8I21 - LOW RESOLUTION DATASET FOR INITIAL PHASING BY SAD
 
Authors :  E. Malito, S. Chandramouli
Date :  02 May 17  (Deposition) - 05 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.99
Chains :  Asym. Unit :  A,B,C,D,E,H,L
Biol. Unit 1:  A (1x),B (1x),C (1x),D (1x),E (1x),H (1x),L (1x)
Keywords :  Hcmv, Neutralizing Epitope, Immunogen, Viral Entry, Pentamer, Vaccine, Immune System, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chandramouli, E. Malito, T. -V. Nguyen, K. Luisi, D. Donnarumma, Y. Xing, N. Norais, D. Yu, A. Carfi
Structural Basis For Potent Antibody-Mediated Neutralizatio Of Human Cytomegalovirus
Sci Immunol 2017
PubMed: search  |  Reference-DOI: 10.1126/SCIIMMUNOL.AAN1457

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN H
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293S
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: GH, UL75
    Organism Common: HHV-5
    Organism Scientific: HUMAN CYTOMEGALOVIRUS
    Organism Taxid: 295027
    Strain: MERLIN
    Synonym: GH
 
Molecule 2 - ENVELOPE GLYCOPROTEIN L
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293S
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: GL, UL115
    Organism Common: HHV-5
    Organism Scientific: HUMAN CYTOMEGALOVIRUS (STRAIN 5508)
    Organism Taxid: 69168
    Strain: 5508
    Synonym: GL
 
Molecule 3 - ENVELOPE GLYCOPROTEIN UL128
    Chains: C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293S
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: UL128
    Organism Common: HHV-5
    Organism Scientific: HUMAN CYTOMEGALOVIRUS (STRAIN AD169)
    Organism Taxid: 10360
    Strain: AD169
 
Molecule 4 - ENVELOPE GLYCOPROTEIN UL130
    Chains: D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293S
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: UL130
    Organism Common: HHV-5
    Organism Scientific: HUMAN CYTOMEGALOVIRUS (STRAIN MERLIN)
    Organism Taxid: 295027
    Strain: MERLIN
 
Molecule 5 - ENVELOPE GLYCOPROTEIN UL131A
    Chains: E
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293S
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: UL131A
    Organism Common: HHV-5
    Organism Scientific: HUMAN CYTOMEGALOVIRUS (STRAIN MERLIN)
    Organism Taxid: 295027
    Strain: MERLIN
 
Molecule 6 - FAB 8I21 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 7 - FAB 8I21 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: IGKV3-15
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IG KAPPA CHAIN V-III REGION CLL,IG KAPPA CHAIN V-III REGION POM

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEHL
Biological Unit 1 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)H (1x)L (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:192 , GLN A:193binding site for Mono-Saccharide NAG A 801 bound to ASN A 192
2AC2SOFTWAREASN A:641 , SER A:643 , LEU A:704 , NAG A:803binding site for Mono-Saccharide NAG A 802 bound to ASN A 641
3AC3SOFTWAREALA A:648 , ASN A:700 , THR A:702 , NAG A:802binding site for Mono-Saccharide NAG A 803 bound to ASN A 700
4AC4SOFTWAREPHE D:71 , SER D:72 , ARG D:117 , ASN D:118binding site for Mono-Saccharide NAG D 301 bound to ASN D 118
5AC5SOFTWAREASN D:201 , HIS E:116binding site for Mono-Saccharide NAG D 302 bound to ASN D 201
6AC6SOFTWARETYR C:130 , ASN E:81 , GLU E:84binding site for Poly-Saccharide residues NAG E 201 through BMA E 203 bound to ASN E 81

(-) SS Bonds  (20, 20)

Asymmetric Unit
No.Residues
1A:59 -B:54
2A:95 -B:47
3A:195 -A:211
4A:330 -A:383
5A:495 -A:522
6A:571 -A:624
7A:647 -A:650
8B:144 -C:162
9B:154 -B:159
10C:30 -C:49
11C:31 -C:64
12C:43 -C:58
13C:96 -C:111
14D:57 -D:83
15D:172 -D:207
16E:20 -E:40
17H:22 -H:96
18H:149 -H:205
19L:23 -L:88
20L:135 -L:195

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Ala A:260 -Pro A:261
2Gly B:80 -Pro B:81
3Ala B:131 -Pro B:132
4Pro B:185 -Pro B:186
5Cys D:57 -Pro D:58
6Phe H:155 -Pro H:156
7Glu H:157 -Pro H:158
8Ser L:7 -Pro L:8
9Tyr L:141 -Pro L:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5VOC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5VOC)

(-) Exons   (0, 0)

(no "Exon" information available for 5VOC)

(-) 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:662
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee...........eee..eeee...eeeeeeee..eeeeeeehhhhhhhhhhhhhhh......hhhhhhhhhh............ee.........................................ee.........eeeee......ee.eeeeeeeeeee......eeeeeee..eeeeeee......eeeeee.....ee....hhhh.eeee....eeeee...hhhhhhhhhh....hhhhhh....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhh.......hhhhhhhhhhh..ee..hhhhhhh....hhhhhhhhhhhhh..................eeee.....eeeeee.......eeee.......eeeeee.................ee.............eeeeeee....eeeeeee.hhhhhhhhhhhhhhh......eeeeee.....eeehhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5voc A  40 LLLNTYGRPIRFLRENTTQCTYNSSLRNSTVVRENAISFNFFQSYNQYYVFHMPRCLFAGPLAEQFLNQVDLTETLERYQQRLNTYALVSKDLASYRSFSQQLKAQDSLGEQPTTVPPPIDLSIPHVWMPPQTTPHESHTTSGLHRPHFNQTCILFDGHDLLFSTVTPCLHQGFYLIDELRYVKITLTEDFFVVTVSIDDDTPMLLIFGHLPRVLFKAPYQRDNFILRQTEKHELLVLVKKDQLNRHSYLKDPDFLDAALDFNYLDLSALLRNSFHRYAVDVLKSGRCQMLDRRTVEMAFAYALALFAAARQEEAGAQVSVPRALDRQAALLQIQEFMITCLSQTPPRTTLLLYPTAVDLAKRALWTPNQITDITSLVRLVYILSKQNQQHLIPQWALRQIADFALKLHKTHLASFLSAFARQELYLMGSLVHSMLVHTTERREIFIVETGLCSLAELSHFTQLLAHPHHEYLSDLYTPCSSSGRRDHSLERLTRLFPATVPAALSILSTMQPSTLETFPDLFCLPLGESFSALTVSEHVSYIVTNQYLIKGISYPVSTTVSLIITQTDSQTKCELTRNMHTTHSITVALNISLENCAFCQSALLEYDDTQGVINIMYMHDSDDVLFALDPYNEVVVSSPRTHYLMLLKNGTVLEVTDVVVD 712
                                    49        59        69        79        89        99       109       119       129       139       149       159       169     ||182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532      |547       557       567       577       587       597       607||     620       630       640       650       660       670       680       690       700       710  
                                                                                                                                                                 175|                                                                                                                                                                                                                                                                                                                                                                     539|                                                            608|                                                                                                    
                                                                                                                                                                  179                                                                                                                                                                                                                                                                                                                                                                      545                                                             612                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhh........................ee.hhh..............hhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhh......eeeee...eeeeee.....ee.hhhhh.eeeeeee...eeeeeeeeee....eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5voc B  37 PTAAEKVPAECPELTRRCLLGEVFEGDKYESWLRPLVNVTGRDGPLSQLIRYRPVTPEAANSVLLDEAFLDTLALLYNNPDQLRALLTLLSSDTAPRWMTVMRGYSECGDGSPAVYTCVDDLCRGYDLTRLSYGRSIFTEHVLGFELVPPSLFNVVVAIRNEATRTNRAVRLPVSTAAAPEGITLFYGLYNAVKEFCLRHQLDPPLLRHLDKYYAGLPPELKQTRVNLPAHSRYGPQ 273
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       


Chain C from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeee.....eeee....eeee...hhhhhhhhhhhhhh..hhhhhhhhhhhhh...eee.....eee.........ee.......eeee...........hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5voc C  29 ECCEFINVNHPPERCYDFKMCNRFTVALRCPDGEVCYSPEKTAEIRGIVTTMTHSLTRQVVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQYLLGAAGSVPYRWINLEYDKITRIVGLDQYLESVKKHKRLDVCR 163
                                    38        48        58        68        78        88        98       108       118       128       138       148       158     


Chain D from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.........hhh.eeeeeeee.hhhhh..eeeeeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh..eeeeeeeeeeee..eeeeeeeeeeeeeee.....eeeeeeeeeee................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5voc D  45 TYSKPHDAATFYCPFLYPSPPRSPLQFSGFQRVSTGPECRNETLYLLYNREGQTLVERSSTWVKKVIWYLSGRNQTILQRMPRTASKPSDGNVQISVEDAKIFGAHMVPKQTKLLRFVVNDGTRYQMCVMKLESWAHVFRDYSVSFQVRLTFTEANNQTYTFCTHPNLIV 214
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214


Chain E from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh.hhhhhhhhhhhhhhh.ee.....eeeeeee...eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5voc E  19 QCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDLTLNYHYDASHGLDNFDVLKRINVTEVSLLISDFRRQNRRGGRTTFNAAGSLAPHARSLEFSVRLFAN 129
                                    28        38        48        58        68        78        88        98 ||    111       121        
                                                                                                           100|                         
                                                                                                            104                         


Chain H from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee....eeeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeeee........eeeeeeeeeee..eeeeeee...ee.ee........eeee....eeeeee.................eee...ee.....eeeeeee...eeeeeee....eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5voc H   1 LVELVESGGGVVQPGRSLRLSCAASGFTFSSDGMHWVRQSPGRGLEWVAFISSDGSTPYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAMYFCAKDWALFRWLRTFDHWGQGTLVTVSSASTKGPSVFPLAPGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTQTYICNVNHKPSNTKVDKRV 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 152       162       172       182       192|      210       220
                                                                                                                                                                135|                                         192|                   
                                                                                                                                                                 148                                          201                   


Chain L from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.......ee...eeeee.......eeeee......eeeeeeee.....eee......eeeee.........eeeeeee.....eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5voc L   1 ETVMTQSPATLSVSPGGRATLSCRASQSVGINLAWYQQKPGQAPRLLIYGASTRASGFPARFSGSGSGTEFTLTITSLQSEDFAVYYCQQYNDWPPWTFGQGTKVEIKRTVAAPSVFIFPPSDESVVCLLNNFYPREAKVQWLQSGNSQESVTEQDSKDSTYSLSSTLTKHKVYACEVTHQGLSSPVTKSFNRG 213
                                    10        20        30        40        50        60        70        80        90       100       110       120   ||  137       147 ||    162       172       189       199       209    
                                                                                                                                                     124|              149|                       181|                        
                                                                                                                                                      132               155                        189
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  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 5VOC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5VOC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5VOC)

(-) Gene Ontology  (11, 22)

Asymmetric Unit(hide GO term definitions)

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

UniProtKB/Swiss-Prot
        GH_HCMVM | Q6SW67: 5vob 5vod
        GL_HCMV8 | Q68674: 5vob 5vod
        Q6GMX0_HUMAN | Q6GMX0: 2d7t 5vob
        S6B291_HUMAN | S6B291: 3mnw 3mnz 4eow 5c7k 5cus 5d9q 5veb 5vic 5vig 5viy 5vj6 5vob 5vod
        U131A_HCMVM | F5HET4: 5vob 5vod
        UL128_HCMVA | P16837: 5vob 5vod
        UL130_HCMVM | F5HCP3: 5vob 5vod
UniProtKB/TrEMBL
        Q6GMX0_HUMAN | Q6GMX0: 1bey
        S6B291_HUMAN | S6B291: 4llw 4lly 4oqt 4ydv

(-) Related Entries Specified in the PDB File

5vob 5vod