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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE IN COMPLEX WITH MG-ADP
 
Authors :  J. B. Thoden, S. M. Firestine, S. J. Benkovic, H. M. Holden
Date :  05 Dec 01  (Deposition) - 28 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Atp-Grasp, Purine Biosynthesis, Nucleotide, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Thoden, S. M. Firestine, S. J. Benkovic, H. M. Holden
Purt-Encoded Glycinamide Ribonucleotide Transformylase. Accommodation Of Adenosine Nucleotide Analogs Within The Active Site.
J. Biol. Chem. V. 277 23898 2002
PubMed-ID: 11953435  |  Reference-DOI: 10.1074/JBC.M202251200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE 2
    Chains: A, B
    EC Number: 2.1.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PURT
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: GART 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 26)

Asymmetric/Biological Unit (6, 26)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL4Ligand/IonCHLORIDE ION
3EDO15Ligand/Ion1,2-ETHANEDIOL
4MG2Ligand/IonMAGNESIUM ION
5MPO1Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID
6NA2Ligand/IonSODIUM ION

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREADP A:1 , GLU A:267 , GLU A:279 , HOH A:485 , HOH A:841BINDING SITE FOR RESIDUE MG A 393
02AC2SOFTWAREGLU B:267 , GLU B:279 , ADP B:397 , HOH B:470 , HOH B:767BINDING SITE FOR RESIDUE MG B 393
03AC3SOFTWAREALA A:53 , HOH A:505 , HOH A:586 , HOH A:811 , HOH A:920 , MET B:50 , HIS B:51 , HOH B:555BINDING SITE FOR RESIDUE NA B 394
04AC4SOFTWAREASN A:100 , VAL A:101 , PRO A:103 , HOH A:432 , HOH A:445 , HOH A:821BINDING SITE FOR RESIDUE NA A 394
05AC5SOFTWAREARG A:43 , VAL A:58 , ARG A:119 , ARG A:133 , PHE A:134 , HOH A:699 , HOH A:809BINDING SITE FOR RESIDUE CL A 395
06AC6SOFTWAREARG A:43 , THR A:131 , TYR A:132 , HOH A:468BINDING SITE FOR RESIDUE CL A 396
07AC7SOFTWAREHIS B:216 , PHE B:217 , HOH B:488 , HOH B:644BINDING SITE FOR RESIDUE CL B 395
08AC8SOFTWAREHOH A:415 , PHE B:337 , GLY B:354BINDING SITE FOR RESIDUE CL B 396
09AC9SOFTWAREARG A:114 , SER A:130 , ILE A:153 , LYS A:155 , GLN A:165 , GLU A:195 , GLY A:196 , VAL A:197 , VAL A:198 , PHE A:200 , GLU A:203 , GLN A:225 , GLU A:267 , PHE A:269 , GLU A:279 , MG A:393 , HOH A:465 , HOH A:479 , HOH A:485 , HOH A:552 , HOH A:556 , HOH A:595 , HOH A:760 , HOH A:841BINDING SITE FOR RESIDUE ADP A 1
10BC1SOFTWAREARG B:114 , SER B:130 , ILE B:153 , LYS B:155 , GLN B:165 , GLU B:195 , GLY B:196 , VAL B:198 , GLU B:203 , GLN B:225 , GLU B:267 , PHE B:269 , GLU B:279 , MG B:393 , HOH B:470 , HOH B:492 , HOH B:505 , HOH B:582 , HOH B:604 , HOH B:756 , HOH B:761 , HOH B:767 , HOH B:775 , HOH B:776BINDING SITE FOR RESIDUE ADP B 397
11BC2SOFTWAREASP A:46 , MET A:50 , HIS A:51 , ARG A:55 , SER A:56 , GLU A:143 , HOH A:460 , HOH A:500 , HOH A:509 , HOH A:688 , LEU B:8 , HIS B:54BINDING SITE FOR RESIDUE MPO A 397
12BC3SOFTWARELEU A:34 , ARG A:305 , HOH A:438 , HOH A:629 , GLN B:349 , ILE B:350BINDING SITE FOR RESIDUE EDO A 398
13BC4SOFTWAREEDO A:406 , HOH A:506 , HOH A:514 , GLU B:30 , ARG B:33 , ASP B:296 , LEU B:297 , SER B:298 , ALA B:301 , HOH B:406 , HOH B:482BINDING SITE FOR RESIDUE EDO B 398
14BC5SOFTWAREILE A:378 , HOH A:934 , HOH B:627BINDING SITE FOR RESIDUE EDO A 399
15BC6SOFTWAREGLY B:21 , GLU B:22 , LEU B:23 , GLY B:24 , GLU B:82 , HOH B:576 , HOH B:709 , HOH B:714 , HOH B:807BINDING SITE FOR RESIDUE EDO B 399
16BC7SOFTWAREARG A:246 , GLU A:274 , VAL A:275 , HOH A:585 , HOH A:680BINDING SITE FOR RESIDUE EDO A 400
17BC8SOFTWAREARG A:69 , HOH A:542 , HOH A:578 , HOH A:877BINDING SITE FOR RESIDUE EDO A 401
18BC9SOFTWARETHR A:2 , LEU A:3 , TYR A:78 , HOH A:549 , HOH A:700 , HOH A:765BINDING SITE FOR RESIDUE EDO A 402
19CC1SOFTWAREPRO B:328 , GLN B:329 , LEU B:330 , VAL B:390 , HOH B:409 , HOH B:483BINDING SITE FOR RESIDUE EDO B 400
20CC2SOFTWAREASN A:60 , ASP A:63 , ALA A:122 , THR A:129 , TYR A:132 , HOH A:568 , HOH A:571 , HOH A:898BINDING SITE FOR RESIDUE EDO A 403
21CC3SOFTWAREGLU A:379 , HIS A:383 , HOH A:456 , HOH A:675 , HOH A:803 , HOH A:947 , HOH A:948BINDING SITE FOR RESIDUE EDO A 404
22CC4SOFTWAREARG A:231 , HOH A:497 , HOH A:589 , HOH A:915 , HOH A:927BINDING SITE FOR RESIDUE EDO A 405
23CC5SOFTWAREPHE B:134 , ALA B:135 , LEU B:140 , ALA B:144 , HOH B:655 , HOH B:787BINDING SITE FOR RESIDUE EDO B 401
24CC6SOFTWARELEU B:244 , GLU B:245 , GLN B:248 , HOH B:559 , HOH B:583BINDING SITE FOR RESIDUE EDO B 402
25CC7SOFTWARELEU A:292 , ILE A:293 , GLN A:349 , ARG A:351 , HOH A:452 , HOH A:478 , HOH A:514 , HOH A:843 , ASP B:296 , EDO B:398BINDING SITE FOR RESIDUE EDO A 406
26CC8SOFTWAREGLY A:64 , ALA A:87 , MET A:90 , GLN A:93BINDING SITE FOR RESIDUE EDO A 407

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Val A:102 -Pro A:103
2Tyr A:150 -Pro A:151
3Gln A:235 -Pro A:236
4Val B:102 -Pro B:103
5Tyr B:150 -Pro B:151
6Gln B:235 -Pro B:236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KJQ)

(-) Exons   (0, 0)

(no "Exon" information available for 1KJQ)

(-) 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:388
 aligned with PURT_ECOLI | P33221 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:391
                                    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 
           PURT_ECOLI     2 TLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGADLQIRLFGKPEIDGSRRLGVALATAESVVDAIERAKHAAGQVKVQG 392
               SCOP domains d1kjqa2 A:2-112 Glycinamide ribonucleotide transformylase PurT, N-domain                                       d1kjqa3 A:113-318 Glycinamide ribonucleotide tr   ansformylase PurT, domain 2                                                                                                                                 d1kjqa1 A:319-392 Glycinamide ribonucleotide transformylase PurT, C-domain SCOP domains
               CATH domains 1kjqA01 A:2-122  [code=3.40.50.20, no name defined]                                                                      1kjqA02 A:123-196 ATP-grasp fold, A d   omain                             1kjqA03 A:197-391 ATP-grasp fold, B domain                                                                                                                                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee..hhhhhhhhhhhhh...eeeeee....hhhhhhh.eeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhh..ee..hhhhhhhhhhhhhhhhhhhh........eeee.hhhhhhhhhhhhh..eeeee...---...eee.hhhhhhhhhhhhhhhhhhhh..eeeee.....eeeeeeeeee..eeee...eeeeee..eeeeeee....hhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..eeeeeeee...hhhhhhhhhhh..hhhhhhhhhhh............eeeeee..eeee...eeehhhhh....eeeee.....eeee...eeeeee..hhhhhhhhhhhhhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kjq A   2 TLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMS---KGQTFIRSAEQLAQAWKYAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGADLQIRLFGKPEIDGSRRLGVALATAESVVDAIERAKHAAGQVKVQG 392
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       | - |     171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
                                                                                                                                                                                       159 163                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:385
 aligned with PURT_ECOLI | P33221 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:391
                                    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 
           PURT_ECOLI     2 TLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGADLQIRLFGKPEIDGSRRLGVALATAESVVDAIERAKHAAGQVKVQG 392
               SCOP domains d1kjqb2 B:2-112 Glycinamide ribonucleotide transformylase PurT, N-domain                                       d1kjqb3 B:113-318 Glycinamide ribonucleotide tr    ansformylase PurT, do  main 2                                                                                                                              d1kjqb1 B:319-392 Glycinamide ribonucleotide transformylase PurT, C-domain SCOP domains
               CATH domains 1kjqB01 B:2-122  [code=3.40.50.20, no name defined]                                                                      1kjqB02 B:123-196 ATP-grasp fold, A d    omain                            1kjqB03 B:197-390 ATP-grasp fold, B domain                                                                                                                                                        -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee..hhhhhhhhhhhhh...eeeeee....hhhhhh..eeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh........eeee.hhhhhhhhhhhhh..eeeee...----..eee.hhhhhhhhhhhhhhh--.....eeeee.....eeeeeeeeee..eeee...eeeeee..eeeeeee....hhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..eeeeeeee...hhhhhhhhhhh..hhhhhhhhhhh............eeeeee..eeee...eeehhhhh....eeeee.....eeee...eeeeee..hhhhhhhhhhhhhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kjq B   2 TLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMS----GQTFIRSAEQLAQAWKYAQQG--AGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGADLQIRLFGKPEIDGSRRLGVALATAESVVDAIERAKHAAGQVKVQG 392
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       | -  |    171       181  |  | 191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
                                                                                                                                                                                       159  164                 184  |                                                                                                                                                                                                             
                                                                                                                                                                                                                   187
   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  (3, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PURT_ECOLI | P33221)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008776    acetate kinase activity    Catalysis of the reaction: ATP + acetate = ADP + acetyl phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016742    hydroxymethyl-, formyl- and related transferase activity    Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0004638    phosphoribosylaminoimidazole carboxylase activity    Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + 2 H(+) = 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO(2).
    GO:0004639    phosphoribosylaminoimidazolesuccinocarboxamide synthase activity    Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate + ATP = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H(+) + phosphate.
    GO:0043815    phosphoribosylglycinamide formyltransferase 2 activity    Catalysis of the reaction: formate + ATP + 5'-phospho-ribosylglycinamide = 5'-phosphoribosyl-N-formylglycinamide + ADP + diphosphate.
    GO:0004644    phosphoribosylglycinamide formyltransferase activity    Catalysis of the reaction: 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006189    'de novo' IMP biosynthetic process    The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
    GO:0046084    adenine biosynthetic process    The chemical reactions and pathways resulting in the formation of adenine, 6-aminopurine, one of the five main bases found in nucleic acids and a component of numerous important derivatives of its corresponding ribonucleoside, adenosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0009152    purine ribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  1kjq
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  PURT_ECOLI | P33221
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  PURT_ECOLI | P33221
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 Related Entries

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        PURT_ECOLI | P33221: 1eyz 1ez1 1kj8 1kj9 1kji 1kjj 1nfe

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1KJQ)