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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF 309M3-B FAB IN COMPLEX WITH H3K9ME3 PEPTIDE
 
Authors :  T. Hattori, I. S. Dementieva, S. P. Montano, S. Koide
Date :  27 Feb 15  (Deposition) - 10 Feb 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.53
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,H,L,P,Q
Keywords :  Antibody, Fab, Head-To-Head Dimerization, H3K9Me3, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Hattori, D. Lai, I. S. Dementieva, S. P. Montano, K. Kurosawa, Y. Zheng, L. R. Akin, K. M. Swist-Rosowska, A. T. Grzybowski, A. Koide, K. Krajewski, B. D. Strahl, N. L. Kelleher, A. J. Ruthenburg, S. Koide
Antigen Clasping By Two Antigen-Binding Sites Of An Exceptionally Specific Antibody For Histone Methylation.
Proc. Natl. Acad. Sci. Usa V. 113 2092 2016
PubMed-ID: 26862167  |  Reference-DOI: 10.1073/PNAS.1522691113

(-) Compounds

Molecule 1 - H3K9ME3 PEPTIDE
    ChainsP, Q
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 2 - FAB HEAVY CHAIN
    ChainsA, C, E, H
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainATCC 55244
    Expression System Taxid562
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - FAB LIGHT CHAIN
    ChainsB, D, L, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainATCC 55244
    Expression System Taxid562
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit ABCDEFHLPQ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1M3L2Mod. Amino AcidN-TRIMETHYLLYSINE

(-) Sites  (0, 0)

(no "Site" information available for 4YHP)

(-) SS Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:96
2A:148 -A:204
3B:22 -B:87
4B:135 -B:195
5C:22 -C:96
6C:148 -C:204
7D:22 -D:87
8D:135 -D:195
9E:22 -E:96
10E:148 -E:204
11F:22 -F:87
12F:135 -F:195
13H:22 -H:96
14H:148 -H:204
15L:22 -L:87
16L:135 -L:195

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Phe A:154 -Pro A:155
2Glu A:156 -Pro A:157
3Tyr B:141 -Pro B:142
4Phe C:154 -Pro C:155
5Glu C:156 -Pro C:157
6Tyr D:141 -Pro D:142
7Phe E:154 -Pro E:155
8Glu E:156 -Pro E:157
9Phe H:154 -Pro H:155
10Glu H:156 -Pro H:157
11Tyr L:141 -Pro L:142
12Tyr F:141 -Pro F:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YHP)

(-) Sequences/Alignments

Asymmetric/Biological 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:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeeee....eeeeee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yhp A   1 EVQLVETGGGVVQPGRSLRLSCTASGFTFRDYWMSWVRQAPGKGLEWVADINPDGITRYYIDAVKGRFTISRDNAKSSLYLQMNSLGAEDTAVYYCAREFHSGLGWHFDLWGRGTLVTVSSASTKGPSVFPLAPSSKSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       143       153       163       173       183       193       203       213         
                                                                                                                                                                   138|                                                                                
                                                                                                                                                                    142                                                                                

Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee....eeee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh..eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yhp B   2 YVLTQPPSVSVAPGQTARITCGGTNIGDISVHWYQQRPGQAPLVVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDDSINAYVFGTGTKVTVLRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  

Chain C from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeeee....eeeeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yhp C   1 EVQLVETGGGVVQPGRSLRLSCTASGFTFRDYWMSWVRQAPGKGLEWVADINPDGITRYYIDAVKGRFTISRDNAKSSLYLQMNSLGAEDTAVYYCAREFHSGLGWHFDLWGRGTLVTVSSASTKGPSVFPLAPSSKGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      |144       154       164       174       184       194       204       214         
                                                                                                                                                                  137|                                                                                 
                                                                                                                                                                   142                                                                                 

Chain D from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeeee....eeee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh....eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yhp D   1 SYVLTQPPSVSVAPGQTARITCGGTNIGDISVHWYQQRPGQAPLVVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDDSINAYVFGTGTKVTVLRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

Chain E from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeeee....eeeeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yhp E   1 EVQLVETGGGVVQPGRSLRLSCTASGFTFRDYWMSWVRQAPGKGLEWVADINPDGITRYYIDAVKGRFTISRDNAKSSLYLQMNSLGAEDTAVYYCAREFHSGLGWHFDLWGRGTLVTVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     ||144       154       164       174       184       194       204       214         
                                                                                                                                                                 136|                                                                                  
                                                                                                                                                                  141                                                                                  

Chain F from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeeee....eeee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yhp F   3 VLTQPPSVSVAPGQTARITCGGTNIGDISVHWYQQRPGQAPLVVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDDSINAYVFGTGTKVTVLRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 213
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212 

Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeee....eeeeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhhh..eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yhp H   1 EVQLVETGGGVVQPGRSLRLSCTASGFTFRDYWMSWVRQAPGKGLEWVADINPDGITRYYIDAVKGRFTISRDNAKSSLYLQMNSLGAEDTAVYYCAREFHSGLGWHFDLWGRGTLVTVSSASTKGPSVFPLAPSSKGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      |144       154       164       174       184       194       204       214        
                                                                                                                                                                  137|                                                                                
                                                                                                                                                                   142                                                                                

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee.........eeeee......eeee.............eeeeee..eeeeee.........eeeeeeee....eeee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yhp L   1 SYVLTQPPSVSVAPGQTARITCGGTNIGDISVHWYQQRPGQAPLVVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDDSINAYVFGTGTKVTVLRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

Chain P from PDB  Type:PROTEIN  Length:11
                                           
               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
                 4yhp P   1 ARTKQTARkST  11
                                    10 
                                    9-M3L

Chain Q from PDB  Type:PROTEIN  Length:11
                                           
               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
                 4yhp Q   1 ARTKQTARkST  11
                                    10 
                                    9-M3L

   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 4YHP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Cis Peptide Bonds
    Glu A:156 - Pro A:157   [ RasMol ]  
    Glu C:156 - Pro C:157   [ RasMol ]  
    Glu E:156 - Pro E:157   [ RasMol ]  
    Glu H:156 - Pro H:157   [ RasMol ]  
    Phe A:154 - Pro A:155   [ RasMol ]  
    Phe C:154 - Pro C:155   [ RasMol ]  
    Phe E:154 - Pro E:155   [ RasMol ]  
    Phe H:154 - Pro H:155   [ RasMol ]  
    Tyr B:141 - Pro B:142   [ RasMol ]  
    Tyr D:141 - Pro D:142   [ RasMol ]  
    Tyr F:141 - Pro F:142   [ RasMol ]  
    Tyr L:141 - Pro L:142   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        H31_HUMAN | P684311cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2lbm 2m0o 2ndf 2ndg 2oq6 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3x1v 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4c1q 4f4u 4f56 4ft2 4ft4 4fwf 4hon 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbr 4qbs 4tn7 4u68 4up0 4uy4 4x3k 4y6l 4yhz 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5d6y 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6

(-) Related Entries Specified in the PDB File

4yhp 4yhz