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(-) Description

Title :  STRUCTURE OF PROSTASIN IN COMPLEX WITH APROTININ
 
Authors :  G. Spraggon, M. Hornsby, A. Shipway, J. L. Harris, S. A. Lesley
Date :  03 Apr 09  (Deposition) - 05 May 09  (Release) - 05 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,I,J
Biol. Unit 1:  A,I  (1x)
Biol. Unit 2:  B,J  (1x)
Keywords :  Prostasin, Hcap1, Channel Activating, Aprotinin, Inhibition, Disulfide Bond, Pharmaceutical, Protease Inhibitor, Secreted, Serine Protease Inhibitor, Cell Membrane, Glycoprotein, Hydrolase, Membrane, Protease, Serine Protease, Transmembrane, Zymogen, Hydrolase/Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Spraggon, M. Hornsby, A. Shipway, D. C. Tully, B. Bursulaya, H. Danahay, J. L. Harris, S. A. Lesley
Active Site Conformational Changes Of Prostasin Provide A New Mechanism Of Protease Regulation By Divalent Cations.
Protein Sci. V. 18 1081 2009
PubMed-ID: 19388054  |  Reference-DOI: 10.1002/PRO.118
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROSTASIN
    ChainsA, B
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System StrainSF9
    Expression System Taxid7108
    FragmentUNP RESIDUES 45-305, PEPTIDASE S1 DOMAIN
    GeneHCAP1, PRSS8
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSERINE PROTEASE 8, PROSTASIN LIGHT CHAIN, PROSTASIN HEAVY CHAIN
 
Molecule 2 - PANCREATIC TRYPSIN INHIBITOR
    ChainsI, J
    EngineeredYES
    Organism CommonBOVINE,COW
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymBASIC PROTEASE INHIBITOR, BPTI, BPI, APROTININ

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABIJ
Biological Unit 1 (1x)A I 
Biological Unit 2 (1x) B J

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3GYM)

(-) Sites  (0, 0)

(no "Site" information available for 3GYM)

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:42 -A:58
2A:136 -A:201
3A:168 -A:182
4A:191 -A:219
5B:42 -B:58
6B:136 -B:201
7B:168 -B:182
8B:191 -B:219
9I:5 -I:55
10I:14 -I:38
11I:30 -I:51
12J:5 -J:55
13J:14 -J:38
14J:30 -J:51

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:144H-Pro A:144I
2Thr B:144H-Pro B:144I

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GYM)

(-) PROSITE Motifs  (5, 10)

Asymmetric Unit (5, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPTI_KUNITZ_2PS50279 Pancreatic trypsin inhibitor (Kunitz) family profile.BPT1_BOVIN40-90
 
  2I:5-55
J:5-55
2TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.PRSS8_HUMAN45-286
 
  2A:16-242
B:16-242
3BPTI_KUNITZ_1PS00280 Pancreatic trypsin inhibitor (Kunitz) family signature.BPT1_BOVIN68-86
 
  2I:33-51
J:33-51
4TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.PRSS8_HUMAN81-86
 
  2A:53-58
B:53-58
5TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.PRSS8_HUMAN232-243
 
  2A:189-200
B:189-200
Biological Unit 1 (5, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPTI_KUNITZ_2PS50279 Pancreatic trypsin inhibitor (Kunitz) family profile.BPT1_BOVIN40-90
 
  1I:5-55
-
2TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.PRSS8_HUMAN45-286
 
  1A:16-242
-
3BPTI_KUNITZ_1PS00280 Pancreatic trypsin inhibitor (Kunitz) family signature.BPT1_BOVIN68-86
 
  1I:33-51
-
4TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.PRSS8_HUMAN81-86
 
  1A:53-58
-
5TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.PRSS8_HUMAN232-243
 
  1A:189-200
-
Biological Unit 2 (5, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPTI_KUNITZ_2PS50279 Pancreatic trypsin inhibitor (Kunitz) family profile.BPT1_BOVIN40-90
 
  1-
J:5-55
2TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.PRSS8_HUMAN45-286
 
  1-
B:16-242
3BPTI_KUNITZ_1PS00280 Pancreatic trypsin inhibitor (Kunitz) family signature.BPT1_BOVIN68-86
 
  1-
J:33-51
4TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.PRSS8_HUMAN81-86
 
  1-
B:53-58
5TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.PRSS8_HUMAN232-243
 
  1-
B:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 3GYM)

(-) 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:241
 aligned with PRSS8_HUMAN | Q16651 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:241
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284 
         PRSS8_HUMAN     45 ITGGSSAVAGQWPWQVSITYEGVHVCGGSLVSEQWVLSAAHCFPSEHHKEAYEVKLGAHQLDSYSEDAKVSTLKDIIPHPSYLQEGSQGDIALLQLSRPITFSRYIRPICLPAANASFPNGLHCTVTGWGHVAPSVSLLTPKPLQQLEVPLISRETCNCLYNIDAKPEEPHFVQEDMVCAGYVEGGKDACQGDSGGPLSCPVEGLWYLTGIVSWGDACGARNRPGVYTLASSYASWIQSKV  285
               SCOP domains d3gyma_ A: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains 3gymA01     3gymA02 A:28-120,A:233-242 Trypsin-like serine proteases                                        3gymA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                                    3gymA02    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeee....eeeehhhhh....hhh.eeeee.............eeeeeeeee.............eeeee..........................eeeeee................eeeeeeeehhhhhhhhhh..............eeee................eeeee....eeeeeeeee..........eeeee...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) TRYPSIN_DOM  PDB: A:16-242 UniProt: 45-286                                                                                                                                                                                                        PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------------------------------TRYPSI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------ PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gym A   16 ITGGSSAVAGQWPWQVSITYEGVHVCGGSLVSEQWVLSAAHCFPSEHHKEAYEVKLGAHQLDSYSEDAKVSTLKDIIPHPSYLQEGSQGDIALLQLSRPITFSRYIRPISLPAAQASFPNGLHCTVTGWGHVAPSVSLLTPKPLQQLEVPLISRETCNSLYNIDAKPEEPHFVQEDMVCAGYVEGGKDACQGDSGGPLSCPVEGLWYLTGIVSWGDACGARNRPGVYTLASSYASWIQSKV  242
                                    25        35||      46        56  |||||58H|       72        82        92       102       112       122       132       142  ||||144H||     161       171 |||||172I|||||  183 ||||||191       201       211       221       231       241 
                                               36|                  58A||||||||                                                                              144A||||||153                172A|||||172J||||   184A|||||                                                      
                                                38                   58B|||||||                                                                               144B|||||||                  172B|||||172K|||    184B||||                                                      
                                                                      58C||||||                                                                                144C||||||                   172C|||||172L||     184C|||                                                      
                                                                       58D|||||                                                                                 144D|||||                    172D|||||172M|      184D||                                                      
                                                                        58E||||                                                                                  144E||||                     172E||||  178       184E|                                                      
                                                                         58F|||                                                                                   144F|||                      172F|||              188                                                      
                                                                          58G||                                                                                    144G||                       172G||                                                                       
                                                                           58H|                                                                                     144H|                        172H|                                                                       
                                                                             63                                                                                      144I                         172I                                                                       

Chain B from PDB  Type:PROTEIN  Length:241
 aligned with PRSS8_HUMAN | Q16651 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:241
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284 
         PRSS8_HUMAN     45 ITGGSSAVAGQWPWQVSITYEGVHVCGGSLVSEQWVLSAAHCFPSEHHKEAYEVKLGAHQLDSYSEDAKVSTLKDIIPHPSYLQEGSQGDIALLQLSRPITFSRYIRPICLPAANASFPNGLHCTVTGWGHVAPSVSLLTPKPLQQLEVPLISRETCNCLYNIDAKPEEPHFVQEDMVCAGYVEGGKDACQGDSGGPLSCPVEGLWYLTGIVSWGDACGARNRPGVYTLASSYASWIQSKV  285
               SCOP domains d3gymb_ B: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains 3gymB01     3gymB02 B:28-120,B:233-242 Trypsin-like serine proteases                                        3gymB01 B:16-27,B:121-232 Trypsin-like serine proteases                                                                    3gymB02    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeee....eeeehhhhh....hhh.eeeee.............eeeeeeeee.............eeeee..........................eeeeee................eeeeeeeehhhhhhhhhh..............eeee................eeeee....eeeeeeeee..........eeeee...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) TRYPSIN_DOM  PDB: B:16-242 UniProt: 45-286                                                                                                                                                                                                        PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------------------------------TRYPSI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------ PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gym B   16 ITGGSSAVAGQWPWQVSITYEGVHVCGGSLVSEQWVLSAAHCFPSEHHKEAYEVKLGAHQLDSYSEDAKVSTLKDIIPHPSYLQEGSQGDIALLQLSRPITFSRYIRPISLPAAQASFPNGLHCTVTGWGHVAPSVSLLTPKPLQQLEVPLISRETCNSLYNIDAKPEEPHFVQEDMVCAGYVEGGKDACQGDSGGPLSCPVEGLWYLTGIVSWGDACGARNRPGVYTLASSYASWIQSKV  242
                                    25        35||      46        56  |||||58H|       72        82        92       102       112       122       132       142  ||||144H||     161       171 |||||172I|||||  183 ||||||191       201       211       221       231       241 
                                               36|                  58A||||||||                                                                              144A||||||153                172A|||||172J||||   184A|||||                                                      
                                                38                   58B|||||||                                                                               144B|||||||                  172B|||||172K|||    184B||||                                                      
                                                                      58C||||||                                                                                144C||||||                   172C|||||172L||     184C|||                                                      
                                                                       58D|||||                                                                                 144D|||||                    172D|||||172M|      184D||                                                      
                                                                        58E||||                                                                                  144E||||                     172E||||  178       184E|                                                      
                                                                         58F|||                                                                                   144F|||                      172F|||              188                                                      
                                                                          58G||                                                                                    144G||                       172G||                                                                       
                                                                           58H|                                                                                     144H|                        172H|                                                                       
                                                                             63                                                                                      144I                         172I                                                                       

Chain I from PDB  Type:PROTEIN  Length:54
 aligned with BPT1_BOVIN | P00974 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:54
                                    46        56        66        76        86    
          BPT1_BOVIN     37 PDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTC   90
               SCOP domains d3gymi_ I: Pancreatic trypsin inhibitor, BPTI          SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh..........eeeeeee....eeeeeee...........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---BPTI_KUNITZ_2  PDB: I:5-55 UniProt: 40-90           PROSITE (1)
                PROSITE (2) ------------------------------------------------------ PROSITE (2)
                PROSITE (3) -------------------------------BPTI_KUNITZ_1      ---- PROSITE (3)
                 Transcript ------------------------------------------------------ Transcript
                3gym I    2 PDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTC   55
                                    11        21        31        41        51    

Chain J from PDB  Type:PROTEIN  Length:54
 aligned with BPT1_BOVIN | P00974 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:54
                                    46        56        66        76        86    
          BPT1_BOVIN     37 PDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTC   90
               SCOP domains d3gymj_ J: Pancreatic trypsin inhibitor, BPTI          SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh..........eeeeeee....eeeeeee...........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---BPTI_KUNITZ_2  PDB: J:5-55 UniProt: 40-90           PROSITE (1)
                PROSITE (2) ------------------------------------------------------ PROSITE (2)
                PROSITE (3) -------------------------------BPTI_KUNITZ_1      ---- PROSITE (3)
                 Transcript ------------------------------------------------------ Transcript
                3gym J    2 PDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTC   55
                                    11        21        31        41        51    

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a3gymA02A:28-120,A:233-242
1b3gymA01A:16-27,A:121-232
1c3gymB01B:16-27,B:121-232
1d3gymB02B:28-120,B:233-242

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GYM)

(-) Gene Ontology  (19, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PRSS8_HUMAN | Q16651)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain I,J   (BPT1_BOVIN | P00974)
molecular function
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0019870    potassium channel inhibitor activity    Stops, prevents, or reduces the activity of a potassium channel.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0090331    negative regulation of platelet aggregation    Any process that decreases the rate, frequency or extent of platelet aggregation. Platelet aggregation is the adhesion of one platelet to one or more other platelets via adhesion molecules.
    GO:0070495    negative regulation of thrombin-activated receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of thrombin-activated receptor protein signaling pathway activity. A thrombin receptor signaling pathway is the series of molecular signals generated as a consequence of a thrombin-activated receptor binding to one of its physiological ligands.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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

UniProtKB/Swiss-Prot
        BPT1_BOVIN | P009741aal 1b0c 1bhc 1bpi 1bpt 1brb 1bth 1bti 1bz5 1bzx 1cbw 1co7 1d0d 1eaw 1ejm 1f5r 1f7z 1fak 1fan 1fy8 1g6x 1jv8 1jv9 1k09 1k6u 1ld5 1ld6 1mtn 1nag 1oa5 1oa6 1p2i 1p2j 1p2k 1p2m 1p2n 1p2o 1p2q 1pit 1qlq 1t7c 1t8l 1t8m 1t8n 1t8o 1tpa 1uua 1uub 1ykt 1ylc 1yld 2fi3 2fi4 2fi5 2ftl 2ftm 2hex 2ijo 2kai 2ptc 2r9p 2ra3 2tgp 2tpi 2zjx 2zvx 3btd 3bte 3btf 3btg 3bth 3btk 3btm 3btq 3btt 3btw 3fp6 3fp7 3fp8 3ldi 3ldj 3ldm 3otj 3p92 3p95 3tgi 3tgj 3tgk 3tpi 3u1j 3wny 4bnr 4dg4 4pti 4tpi 4wwy 4wxv 4y0y 4y0z 4y10 4y11 5jb4 5jb5 5jb6 5jb7 5pti 6pti 7pti 8pti 9pti
        PRSS8_HUMAN | Q166513dfj 3dfl 3e0n 3e0p 3e16 3e1x 3fvf 3gyl

(-) Related Entries Specified in the PDB File

3e1x 3eon 3fvf 3gyl