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(-) Description

Title :  STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE
 
Authors :  H. -W. Park, A. Sancar, J. Deisenhofer
Date :  03 Jul 95  (Deposition) - 01 Aug 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dna Repair, Electron Transfer, Excitation Energy Transfer, Lyase, Carbon-Carbon, Lyase (Carbon-Carbon) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. W. Park, S. T. Kim, A. Sancar, J. Deisenhofer
Crystal Structure Of Dna Photolyase From Escherichia Coli.
Science V. 268 1866 1995
PubMed-ID: 7604260
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA PHOTOLYASE
    ChainsA, B
    EC Number4.1.99.3
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsPHOTOREACTIVATING ENZYME
    SynonymDNA CYCLOBUTANE DIPYRIMIDINE PHOTOLYASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MHF2Ligand/Ion5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MHF1Ligand/Ion5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MHF1Ligand/Ion5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:222 , THR A:234 , SER A:235 , ARG A:236 , LEU A:237 , SER A:238 , TRP A:271 , GLU A:274 , ARG A:278 , TYR A:281 , TRP A:338 , ASN A:341 , ARG A:344 , LEU A:370 , ASP A:372 , GLY A:373 , ASP A:374 , ALA A:377 , ASN A:378 , GLY A:381 , TRP A:382 , HOH A:514 , HOH A:526 , HOH A:617 , HOH A:704 , HOH A:747 , HOH A:835BINDING SITE FOR RESIDUE FAD A 472
2AC2SOFTWAREHIS A:44 , GLU A:106 , ASN A:108 , GLU A:109 , CYS A:292 , LYS A:293BINDING SITE FOR RESIDUE MHF A 473
3AC3SOFTWARETYR B:222 , THR B:234 , SER B:235 , ARG B:236 , LEU B:237 , SER B:238 , TRP B:271 , GLU B:274 , ARG B:278 , TYR B:281 , TRP B:338 , ASN B:341 , ARG B:344 , LEU B:370 , ASP B:372 , GLY B:373 , ASP B:374 , ALA B:377 , ASN B:378 , GLY B:381 , HOH B:511 , HOH B:553 , HOH B:596 , HOH B:689 , HOH B:797BINDING SITE FOR RESIDUE FAD B 472
4AC4SOFTWAREHIS B:44 , GLU B:106 , ASN B:108 , GLU B:109 , CYS B:292 , LYS B:293 , GLY B:441 , THR B:443 , HOH B:813BINDING SITE FOR RESIDUE MHF B 473

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DNP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DNP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DNP)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHR_CRY_ALPHA_BETAPS51645 Photolyase/cryptochrome alpha/beta domain profile.PHR_ECOLI2-134
 
  2A:1-133
B:1-133
2DNA_PHOTOLYASES_1_1PS00394 DNA photolyases class 1 signature 1.PHR_ECOLI322-334
 
  2A:321-333
B:321-333
3DNA_PHOTOLYASES_1_2PS00691 DNA photolyases class 1 signature 2.PHR_ECOLI342-361
 
  2A:341-360
B:341-360
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHR_CRY_ALPHA_BETAPS51645 Photolyase/cryptochrome alpha/beta domain profile.PHR_ECOLI2-134
 
  1A:1-133
-
2DNA_PHOTOLYASES_1_1PS00394 DNA photolyases class 1 signature 1.PHR_ECOLI322-334
 
  1A:321-333
-
3DNA_PHOTOLYASES_1_2PS00691 DNA photolyases class 1 signature 2.PHR_ECOLI342-361
 
  1A:341-360
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHR_CRY_ALPHA_BETAPS51645 Photolyase/cryptochrome alpha/beta domain profile.PHR_ECOLI2-134
 
  1-
B:1-133
2DNA_PHOTOLYASES_1_1PS00394 DNA photolyases class 1 signature 1.PHR_ECOLI322-334
 
  1-
B:321-333
3DNA_PHOTOLYASES_1_2PS00691 DNA photolyases class 1 signature 2.PHR_ECOLI342-361
 
  1-
B:341-360

(-) Exons   (0, 0)

(no "Exon" information available for 1DNP)

(-) 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:469
 aligned with PHR_ECOLI | P00914 from UniProtKB/Swiss-Prot  Length:472

    Alignment length:469
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461         
            PHR_ECOLI     2 TTHLVWFRQDLRLHDNLALAAACRNSSARVLALYIATPRQWATHNMSPRQAELINAQLNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVERALRNVVCEGFDDSVILPPGAVMTGNHEMYKVFTPFKNAWLKRLREGMPECVAAPKVRSSGSIEPSPSITLNYPRQSFDTAHFPVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLSASLATGGLSPRQCLHRLLAEQPQALDGGAGSVWLNELIWREFYRHLITYHPSLCKHRPFIAWTDRVQWQSNPAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGEKFDHEGEFIRQWLPELRDVPGKVVHEPWKWAQKAGVTLDYPQPIVEHKEARVQTLAAYEAARK 470
               SCOP domains d1dnpa2 A:1-200 DNA photolyase                                                                                                                                                                          d1dnpa1 A:201-469 C-terminal domain of DNA photolyase                                                                                                                                                                                                                         SCOP domains
               CATH domains 1dnpA01 A:1-130 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                             1dnpA02 A:131-168,A:204-288           -----------------------------------1dnpA02 A:131-168,A:204-288  [code=1.25.40.80, no name defined]                      1dnpA03 A:289-469 DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........hhhhhh......eeeeeeeeehhhhhh....hhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh....eeeee.....................hhhhhhhhhhhhh.........................................hhhhhhhhhhhhh.hhhhhhhh............hhhhhh....hhhhhhhhhhh.hhhhh....hhhhhhhhhhhhhhhhhhh.hhhh......hhhhh......hhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhh.....hhhhhhhhh.......hhhhhhhhhhh...............hhhhhhhh....hhhhhh.hhh......hhhhhhhhhhhh............hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PHR_CRY_ALPHA_BETA  PDB: A:1-133 UniProt: 2-134                                                                                      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_PHOTOLYAS-------DNA_PHOTOLYASES_1_2 ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dnp A   1 TTHLVWFRQDLRLHDNLALAAACRNSSARVLALYIATPRQWATHNMSPRQAELINAQLNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVERALRNVVCEGFDDSVILPPGAVMTGNHEMYKVFTPFKNAWLKRLREGMPECVAAPKVRSSGSIEPSPSITLNYPRQSFDTAHFPVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLSASLATGGLSPRQCLHRLLAEQPQALDGGAGSVWLNELIWREFYRHLITYHPSLCKHRPFIAWTDRVQWQSNPAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGEKFDHEGEFIRQWLPELRDVPGKVVHEPWKWAQKAGVTLDYPQPIVEHKEARVQTLAAYEAARK 469
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460         

Chain B from PDB  Type:PROTEIN  Length:469
 aligned with PHR_ECOLI | P00914 from UniProtKB/Swiss-Prot  Length:472

    Alignment length:469
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461         
            PHR_ECOLI     2 TTHLVWFRQDLRLHDNLALAAACRNSSARVLALYIATPRQWATHNMSPRQAELINAQLNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVERALRNVVCEGFDDSVILPPGAVMTGNHEMYKVFTPFKNAWLKRLREGMPECVAAPKVRSSGSIEPSPSITLNYPRQSFDTAHFPVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLSASLATGGLSPRQCLHRLLAEQPQALDGGAGSVWLNELIWREFYRHLITYHPSLCKHRPFIAWTDRVQWQSNPAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGEKFDHEGEFIRQWLPELRDVPGKVVHEPWKWAQKAGVTLDYPQPIVEHKEARVQTLAAYEAARK 470
               SCOP domains d1dnpb2 B:1-200 DNA photolyase                                                                                                                                                                          d1dnpb1 B:201-469 C-terminal domain of DNA photolyase                                                                                                                                                                                                                         SCOP domains
               CATH domains 1dnpB01 B:1-130 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                             1dnpB02 B:131-168,B:204-288           -----------------------------------1dnpB02 B:131-168,B:204-288  [code=1.25.40.80, no name defined]                      1dnpB03 B:289-469 DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........hhhhhh......eeeeeeeeehhhhhh....hhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh....eeeee.....................hhhhhhhhhhhhhh........................................hhhhhhhhhhhhh.hhhhhhhh............hhhhhh....hhhhhhhhhhh.hhhhh....hhhhhhhhhhhhhhhhhhh.hhhhh.....hhhhh......hhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhh.....hhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhh....hhhhhh.hhh.......hhhhhhhhhhh............hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PHR_CRY_ALPHA_BETA  PDB: B:1-133 UniProt: 2-134                                                                                      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_PHOTOLYAS-------DNA_PHOTOLYASES_1_2 ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dnp B   1 TTHLVWFRQDLRLHDNLALAAACRNSSARVLALYIATPRQWATHNMSPRQAELINAQLNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVERALRNVVCEGFDDSVILPPGAVMTGNHEMYKVFTPFKNAWLKRLREGMPECVAAPKVRSSGSIEPSPSITLNYPRQSFDTAHFPVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLSASLATGGLSPRQCLHRLLAEQPQALDGGAGSVWLNELIWREFYRHLITYHPSLCKHRPFIAWTDRVQWQSNPAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGEKFDHEGEFIRQWLPELRDVPGKVVHEPWKWAQKAGVTLDYPQPIVEHKEARVQTLAAYEAARK 469
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460         

   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  (3, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DNP)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PHR_ECOLI | P00914)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003904    deoxyribodipyrimidine photo-lyase activity    Catalysis of the reaction: cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA). This reaction represents the reactivation of irradiated DNA by light.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.

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