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(-) Description

Title :  CRYSTAL STRUCTURE OF TT1595, A PUTATIVE SAM-DEPENDENT METHYLTRANSFERASE FROM THERMUS THERMOPHILLUS HB8
 
Authors :  A. A. Pioszak, K. Murayama, N. Nakagawa, A. Ebihara, S. Kuramitsu, M. Sh S. Yokoyama, Riken Structural Genomics/Proteomics Initiative
Date :  02 Feb 05  (Deposition) - 02 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Biol. Unit 3:  D  (2x)
Keywords :  Thermus Thermophillus, Methyltransferase, Adomet, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. A. Pioszak, K. Murayama, N. Nakagawa, A. Ebihara, S. Kuramitsu, M. Shirouzu, S. Yokoyama
Structures Of A Putative Rna 5-Methyluridine Methyltransferase, Thermus Thermophilus Ttha1280, And Its Complex With S-Adenosyl-L-Homocysteine.
Acta Crystallogr. , Sect. F V. 61 867 2005
PubMed-ID: 16511182  |  Reference-DOI: 10.1107/S1744309105029842

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN TTHA1280
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11
    Expression System StrainB834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid300852
    StrainHB8
    SynonymTT1595

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (2x)  C 
Biological Unit 3 (2x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1HEZ1Ligand/IonHEXANE-1,6-DIOL
2MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1HEZ-1Ligand/IonHEXANE-1,6-DIOL
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1HEZ2Ligand/IonHEXANE-1,6-DIOL
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1HEZ-1Ligand/IonHEXANE-1,6-DIOL
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER C:15BINDING SITE FOR RESIDUE HEZ C 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WXW)

(-) 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:377
 aligned with Q5SIT4_THET8 | Q5SIT4 from UniProtKB/TrEMBL  Length:382

    Alignment length:382
                                    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  
         Q5SIT4_THET8     1 MRIQVNAKGAARLLSRHLWVFRRDVVSGPETPGLYPVYWGRRFLALALYNPHTDLAVRAYRFAPAEDPVAALLENLAQALARREAVLRQDPEGGYRLVHAEGDLLPGLVVDYYAGHAVVQATAHAWEGLLPQVAEALRPHVQSVLAKNDARTRELEGLPLYVRPLLGEVPERVQVQEGRVRYLVDLRAGQKTGAYLDQRENRLYMERFRGERALDVFSYAGGFALHLALGFREVVAVDSSAEALRRAEENARLNGLGNVRVLEANAFDLLRRLEKEGERFDLVVLDPPAFAKGKKDVERAYRAYKEVNLRAIKLLKEGGILATASCSHHMTEPLFYAMVAEAAQDAHRLLRVVEKRGQPFDHPVLLNHPETHYLKFAVFQVL 382
               SCOP domains d1wxwa1 A:1-64 Hypothetical protein TTHA1280, N-terminal domain d1wxwa2 A:65-382 Hypothetical protein TTHA1280, middle and C-terminal domains                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------1wxwA03 A:172-382      Vaccinia Virus protein VP39                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhh...eee...eee.....eeeeeee..eeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhh...eeeeee..eeeeee.hhhhh.hhhhhhhhhh....eeeeee.hhhhh......eeeeeee.....eeeee..eeeee....-----.hhhhhhhhhhhhhh.eeeeeee....hhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee.....hhhhhhhhhhhhhhhh...eeeeeee...........hhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wxw A   1 mRIQVNAKGAARLLSRHLWVFRRDVVSGPETPGLYPVYWGRRFLALALYNPHTDLAVRAYRFAPAEDPVAALLENLAQALARREAVLRQDPEGGYRLVHAEGDLLPGLVVDYYAGHAVVQATAHAWEGLLPQVAEALRPHVQSVLAKNDARTRELEGLPLYVRPLLGEVPERVQVQEGRVRYLVDLRA-----AYLDQRENRLYmERFRGERALDVFSYAGGFALHLALGFREVVAVDSSAEALRRAEENARLNGLGNVRVLEANAFDLLRRLEKEGERFDLVVLDPPAFAKGKKDVERAYRAYKEVNLRAIKLLKEGGILATASCSHHmTEPLFYAmVAEAAQDAHRLLRVVEKRGQPFDHPVLLNHPETHYLKFAVFQVL 382
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       | -   |   200    |  210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380  
                            |                                                                                                                                                                                        188   194        205-MSE                                                                                                                      330-MSE 338-MSE                                        
                            1-MSE                                                                                                                                                                                                                                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:382
 aligned with Q5SIT4_THET8 | Q5SIT4 from UniProtKB/TrEMBL  Length:382

    Alignment length:382
                                    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  
         Q5SIT4_THET8     1 MRIQVNAKGAARLLSRHLWVFRRDVVSGPETPGLYPVYWGRRFLALALYNPHTDLAVRAYRFAPAEDPVAALLENLAQALARREAVLRQDPEGGYRLVHAEGDLLPGLVVDYYAGHAVVQATAHAWEGLLPQVAEALRPHVQSVLAKNDARTRELEGLPLYVRPLLGEVPERVQVQEGRVRYLVDLRAGQKTGAYLDQRENRLYMERFRGERALDVFSYAGGFALHLALGFREVVAVDSSAEALRRAEENARLNGLGNVRVLEANAFDLLRRLEKEGERFDLVVLDPPAFAKGKKDVERAYRAYKEVNLRAIKLLKEGGILATASCSHHMTEPLFYAMVAEAAQDAHRLLRVVEKRGQPFDHPVLLNHPETHYLKFAVFQVL 382
               SCOP domains d1wxwb1 B:1-64 Hypothetical protein TTHA1280, N-terminal domain d1wxwb2 B:65-382 Hypothetical protein TTHA1280, middle and C-terminal domains                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------1wxwB03 B:172-382 Vaccinia Virus protein VP39                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhh...eehhh.eee.....eeeeeee..eeeeeeee.......eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhh...eeeeee..eeeeee.hhhhh.hhhhhhhhhhhhh.eeeeee..hhhhhh....eeeeee.....eeeeee..eeeeee.........hhhhhhhhhhhhhh.eeeeeee....hhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhhhhhhheeeeeeeeeee.....hhhhhhhhhhhhhhhh...eeeeeee...........hhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wxw B   1 mRIQVNAKGAARLLSRHLWVFRRDVVSGPETPGLYPVYWGRRFLALALYNPHTDLAVRAYRFAPAEDPVAALLENLAQALARREAVLRQDPEGGYRLVHAEGDLLPGLVVDYYAGHAVVQATAHAWEGLLPQVAEALRPHVQSVLAKNDARTRELEGLPLYVRPLLGEVPERVQVQEGRVRYLVDLRAGQKTGAYLDQRENRLYmERFRGERALDVFSYAGGFALHLALGFREVVAVDSSAEALRRAEENARLNGLGNVRVLEANAFDLLRRLEKEGERFDLVVLDPPAFAKGKKDVERAYRAYKEVNLRAIKLLKEGGILATASCSHHmTEPLFYAmVAEAAQDAHRLLRVVEKRGQPFDHPVLLNHPETHYLKFAVFQVL 382
                            |       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  
                            1-MSE                                                                                                                                                                                                     205-MSE                                                                                                                      330-MSE 338-MSE                                        

Chain C from PDB  Type:PROTEIN  Length:382
 aligned with Q5SIT4_THET8 | Q5SIT4 from UniProtKB/TrEMBL  Length:382

    Alignment length:382
                                    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  
         Q5SIT4_THET8     1 MRIQVNAKGAARLLSRHLWVFRRDVVSGPETPGLYPVYWGRRFLALALYNPHTDLAVRAYRFAPAEDPVAALLENLAQALARREAVLRQDPEGGYRLVHAEGDLLPGLVVDYYAGHAVVQATAHAWEGLLPQVAEALRPHVQSVLAKNDARTRELEGLPLYVRPLLGEVPERVQVQEGRVRYLVDLRAGQKTGAYLDQRENRLYMERFRGERALDVFSYAGGFALHLALGFREVVAVDSSAEALRRAEENARLNGLGNVRVLEANAFDLLRRLEKEGERFDLVVLDPPAFAKGKKDVERAYRAYKEVNLRAIKLLKEGGILATASCSHHMTEPLFYAMVAEAAQDAHRLLRVVEKRGQPFDHPVLLNHPETHYLKFAVFQVL 382
               SCOP domains d1wxwc1 C:1-64 Hypothetical protein TTHA1280, N-terminal domain d1wxwc2 C:65-382 Hypothetical protein TTHA1280, middle and C-terminal domains                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------1wxwC03 C:172-382 Vaccinia Virus protein VP39                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhh...eee...eee.....eeeeeee..eeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhh...eeeeee..eeeeee.hhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhh.....eeeeee.....eeeeee..eeeeee.........hhhhhhhhhhhhhh.eeeeeee....hhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhhhhhhheeeeeeeeeee.....hhhhhhhhhhhhhhhh...eeeeeee...........hhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wxw C   1 mRIQVNAKGAARLLSRHLWVFRRDVVSGPETPGLYPVYWGRRFLALALYNPHTDLAVRAYRFAPAEDPVAALLENLAQALARREAVLRQDPEGGYRLVHAEGDLLPGLVVDYYAGHAVVQATAHAWEGLLPQVAEALRPHVQSVLAKNDARTRELEGLPLYVRPLLGEVPERVQVQEGRVRYLVDLRAGQKTGAYLDQRENRLYmERFRGERALDVFSYAGGFALHLALGFREVVAVDSSAEALRRAEENARLNGLGNVRVLEANAFDLLRRLEKEGERFDLVVLDPPAFAKGKKDVERAYRAYKEVNLRAIKLLKEGGILATASCSHHmTEPLFYAmVAEAAQDAHRLLRVVEKRGQPFDHPVLLNHPETHYLKFAVFQVL 382
                            |       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  
                            1-MSE                                                                                                                                                                                                     205-MSE                                                                                                                      330-MSE 338-MSE                                        

Chain D from PDB  Type:PROTEIN  Length:382
 aligned with Q5SIT4_THET8 | Q5SIT4 from UniProtKB/TrEMBL  Length:382

    Alignment length:382
                                    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  
         Q5SIT4_THET8     1 MRIQVNAKGAARLLSRHLWVFRRDVVSGPETPGLYPVYWGRRFLALALYNPHTDLAVRAYRFAPAEDPVAALLENLAQALARREAVLRQDPEGGYRLVHAEGDLLPGLVVDYYAGHAVVQATAHAWEGLLPQVAEALRPHVQSVLAKNDARTRELEGLPLYVRPLLGEVPERVQVQEGRVRYLVDLRAGQKTGAYLDQRENRLYMERFRGERALDVFSYAGGFALHLALGFREVVAVDSSAEALRRAEENARLNGLGNVRVLEANAFDLLRRLEKEGERFDLVVLDPPAFAKGKKDVERAYRAYKEVNLRAIKLLKEGGILATASCSHHMTEPLFYAMVAEAAQDAHRLLRVVEKRGQPFDHPVLLNHPETHYLKFAVFQVL 382
               SCOP domains d1wxwd1 D:1-64 Hypothetical protein TTHA1280, N-terminal domain d1wxwd2 D:65-382 Hypothetical protein TTHA1280, middle and C-terminal domains                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------1wxwD03 D:172-382 Vaccinia Virus protein VP39                                                                                                                                                                       CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------Methyltrans_SAM-1wxwD01 D:95-365                                                                                                                                                                                                                                               ----------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------Methyltrans_SAM-1wxwD02 D:95-365                                                                                                                                                                                                                                               ----------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------Methyltrans_SAM-1wxwD03 D:95-365                                                                                                                                                                                                                                               ----------------- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------Methyltrans_SAM-1wxwD04 D:95-365                                                                                                                                                                                                                                               ----------------- Pfam domains (4)
         Sec.struct. author ..eeehhhhhhhhhh...eee...eee.....eeeeeee..eeeeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhh...eeeeee..eeeeee.hhhhhhhhhhhhhhhhhhh.eeee...hhhhhhh......eeeee....eeeeee..eeeeee.........hhhhhhhhhhhhhh.eeeeeee....hhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhhhhhhheeeeeeeeeee.....hhhhhhhhhhhhhhhh...eeeeeee...........hhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wxw D   1 mRIQVNAKGAARLLSRHLWVFRRDVVSGPETPGLYPVYWGRRFLALALYNPHTDLAVRAYRFAPAEDPVAALLENLAQALARREAVLRQDPEGGYRLVHAEGDLLPGLVVDYYAGHAVVQATAHAWEGLLPQVAEALRPHVQSVLAKNDARTRELEGLPLYVRPLLGEVPERVQVQEGRVRYLVDLRAGQKTGAYLDQRENRLYmERFRGERALDVFSYAGGFALHLALGFREVVAVDSSAEALRRAEENARLNGLGNVRVLEANAFDLLRRLEKEGERFDLVVLDPPAFAKGKKDVERAYRAYKEVNLRAIKLLKEGGILATASCSHHmTEPLFYAmVAEAAQDAHRLLRVVEKRGQPFDHPVLLNHPETHYLKFAVFQVL 382
                            |       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  
                            1-MSE                                                                                                                                                                                                     205-MSE                                                                                                                      330-MSE 338-MSE                                        

   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 8)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q5SIT4_THET8 | Q5SIT4)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/TrEMBL
        Q5SIT4_THET8 | Q5SIT41wxx 2cww

(-) Related Entries Specified in the PDB File

1wxx ALTERNATE CRYSTAL FORM OF THE SAME PROTEIN RELATED ID: TTK003001595 RELATED DB: TARGETDB