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(-) Description

Title :  SOLUTION STRUCTURE OF HUMAN 53BP1 TANDEM TUDOR DOMAINS IN COMPLEX WITH A HISTONE H4K20ME2 PEPTIDE
 
Authors :  G. Cui, M. Botuyan, G. Mer
Date :  07 Jul 12  (Deposition) - 12 Dec 12  (Release) - 03 Apr 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Dimethylation, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Tang, N. W. Cho, G. Cui, E. M. Manion, N. M. Shanbhag, M. V. Botuyan, G. Mer, R. A. Greenberg
Acetylation Limits 53Bp1 Association With Damaged Chromatin To Promote Homologous Recombination.
Nat. Struct. Mol. Biol. V. 20 317 2013
PubMed-ID: 23377543  |  Reference-DOI: 10.1038/NSMB.2499

(-) Compounds

Molecule 1 - TUMOR SUPPRESSOR P53-BINDING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPTEV
    FragmentUNP RESIDUES 1484-1603
    GeneTP53BP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym53BP1, P53-BINDING PROTEIN 1, P53BP1
 
Molecule 2 - HISTONE H4
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPGB1
    FragmentUNP RESIDUES 15-28
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1MLY1Mod. Amino AcidN-DIMETHYL-LYSINE
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1MLY1Mod. Amino AcidN-DIMETHYL-LYSINE

(-) Sites  (0, 0)

(no "Site" information available for 2LVM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2LVM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2LVM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038689G1488WTP53B_HUMANPolymorphism11554564AG1488W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038689G1488WTP53B_HUMANPolymorphism11554564AG1488W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_H4PS00047 Histone H4 signature.H4_HUMAN15-19  1B:14-18
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_H4PS00047 Histone H4 signature.H4_HUMAN15-19  1B:14-18

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002638011bENSE00001344404chr15:43802812-43802568245TP53B_HUMAN-00--
1.4ENST000002638014ENSE00001713374chr15:43784666-43784482185TP53B_HUMAN1-59590--
1.5ENST000002638015ENSE00001046179chr15:43784293-4378420094TP53B_HUMAN60-91320--
1.6ENST000002638016ENSE00001046160chr15:43783951-4378386785TP53B_HUMAN91-119290--
1.7ENST000002638017ENSE00001046169chr15:43773220-43773093128TP53B_HUMAN119-162440--
1.8ENST000002638018ENSE00001046152chr15:43772215-43772057159TP53B_HUMAN162-215540--
1.9ENST000002638019ENSE00001046208chr15:43771724-43771595130TP53B_HUMAN215-258440--
1.10ENST0000026380110ENSE00001046166chr15:43769957-43769791167TP53B_HUMAN258-314570--
1.11ENST0000026380111ENSE00001046193chr15:43767892-43767763130TP53B_HUMAN314-357440--
1.12ENST0000026380112ENSE00001046180chr15:43766965-4376687195TP53B_HUMAN357-389330--
1.13ENST0000026380113ENSE00001046161chr15:43762264-43762056209TP53B_HUMAN389-458700--
1.14aENST0000026380114aENSE00001046204chr15:43749416-437480901327TP53B_HUMAN459-9014430--
1.15aENST0000026380115aENSE00001046164chr15:43739683-43739564120TP53B_HUMAN901-941410--
1.17ENST0000026380117ENSE00001628086chr15:43738788-43738585204TP53B_HUMAN941-1009690--
1.18aENST0000026380118aENSE00001675565chr15:43733781-4373372458TP53B_HUMAN1009-1028200--
1.19aENST0000026380119aENSE00001595850chr15:43730614-4373052293TP53B_HUMAN1028-1059320--
1.20bENST0000026380120bENSE00001729133chr15:43724875-43724392484TP53B_HUMAN1059-12201620--
1.21aENST0000026380121aENSE00001648704chr15:43720366-43720214153TP53B_HUMAN1221-1271510--
1.22aENST0000026380122aENSE00001612038chr15:43714324-43714053272TP53B_HUMAN1272-1362910--
1.23bENST0000026380123bENSE00001657667chr15:43713372-43713223150TP53B_HUMAN1362-1412510--
1.24aENST0000026380124aENSE00001735071chr15:43712933-43712503431TP53B_HUMAN1412-15561451A:-3-155676
1.25bENST0000026380125bENSE00001666968chr15:43708614-43708423192TP53B_HUMAN1556-1620651A:1556-160348
1.26ENST0000026380126ENSE00001684657chr15:43708007-43707792216TP53B_HUMAN1620-1692730--
1.28bENST0000026380128bENSE00001734669chr15:43705532-43705317216TP53B_HUMAN1692-1764730--
1.30ENST0000026380130ENSE00001771292chr15:43701939-4370184595TP53B_HUMAN1764-1795320--
1.31bENST0000026380131bENSE00001727562chr15:43701294-43701095200TP53B_HUMAN1796-1862670--
1.32ENST0000026380132ENSE00001751396chr15:43700286-43700141146TP53B_HUMAN1862-1911500--
1.33bENST0000026380133bENSE00001841464chr15:43699768-43699407362TP53B_HUMAN1911-1972620--

2.1ENST000003778031ENSE00001475159chr6:26104104-26104518415H4_HUMAN1-1271271B:14-2714

(-) Sequences/Alignments

NMR Structure
   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:123
 aligned with TP53B_HUMAN | Q12888 from UniProtKB/Swiss-Prot  Length:1972

    Alignment length:123
                                  1490      1500      1510      1520      1530      1540      1550      1560      1570      1580      1590      1600   
         TP53B_HUMAN   1481 SPGNSFVGLRVVAKWSSNGYFYSGKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIPLDTEVTALSEDEYFSAGVVKGHRKESGELYYSIEKEGQRKWYKRMAVILSLEQGNRLREQYGLG 1603
               SCOP domains d2lvma1 A:-3-1537 p53-binding protein 1, 53BP1           d2lvma2 A:1538-1603 p53-binding protein 1, 53BP1                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee......eeeeeeeeeee..eeeeee....eeeee...ee.........eeeee.....eeeeee...eee..eeeeeeee..eeeeee...ee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------W------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.24a  PDB: A:-3-1556 UniProt: 1412-1556 [INCOMPLETE]                  ----------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------Exon 1.25b  PDB: A:1556-1603 UniProt: 1556-1620  Transcript 1 (2)
                2lvm A   -3 GHMNSFVGLRVVAKWSSNGYFYSGKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIPLDTEVTALSEDEYFSAGVVKGHRKESGELYYSIEKEGQRKWYKRMAVILSLEQGNRLREQYGLG 1603
                              ||  1490      1500      1510      1520      1530      1540      1550      1560      1570      1580      1590      1600   
                             -1|                                                                                                                       
                            1484                                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:14
 aligned with H4_HUMAN | P62805 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:14
                                    24    
            H4_HUMAN     15 GAKRHRKVLRDNIQ   28
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE HISTO--------- PROSITE
               Transcript 2 Exon 2.1       Transcript 2
                2lvm B   14 GAKRHRkVLRDNIQ   27
                                  | 23    
                                 20-MLY   

   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  (1, 2)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2LVM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2LVM)

(-) Gene Ontology  (50, 56)

NMR Structure(hide GO term definitions)
Chain A   (TP53B_HUMAN | Q12888)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001102    RNA polymerase II activating transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
    GO:0001104    RNA polymerase II transcription cofactor activity    Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between regulatory transcription factors and the basal RNAP II transcription machinery.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    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).
biological process
    GO:0000077    DNA damage checkpoint    A cell cycle checkpoint that regulates progression through the cell cycle in response to DNA damage. A DNA damage checkpoint may blocks cell cycle progression (in G1, G2 or metaphase) or slow the rate at which S phase proceeds.
    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:0071481    cellular response to X-ray    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 X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz).
    GO:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000777    condensed chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain B   (H4_HUMAN | P62805)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0034080    CENP-A containing nucleosome assembly    The formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres.
    GO:0006335    DNA replication-dependent nucleosome assembly    The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
    GO:0006336    DNA replication-independent nucleosome assembly    The formation of nucleosomes outside the context of DNA replication.
    GO:0006352    DNA-templated transcription, initiation    Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
    GO:1904837    beta-catenin-TCF complex assembly    The aggregation, arrangement and bonding together of a set of components to form a beta-catenin-TCF complex.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0045814    negative regulation of gene expression, epigenetic    Any epigenetic process that stops, prevents or reduces the rate of gene expression.
    GO:0045653    negative regulation of megakaryocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0045815    positive regulation of gene expression, epigenetic    Any epigenetic process that activates or increases the rate of gene expression.
    GO:0051290    protein heterotetramerization    The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
    GO:0016233    telomere capping    A process in which telomeres are protected from degradation and fusion, thereby ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. May be mediated by specific single- or double-stranded telomeric DNA binding proteins.
    GO:0032200    telomere organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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

UniProtKB/Swiss-Prot
        H4_HUMAN | P628051kx4 1kx5 1m18 1m19 1m1a 1s32 1zkk 2bqz 2cv5 2ig0 2kwn 2kwo 2qqs 2rje 2rny 2rs9 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3cfs 3cfv 3f9w 3f9x 3f9y 3f9z 3ij1 3jpx 3nqj 3nqu 3o36 3qby 3qzs 3qzt 3qzv 3r45 3uvw 3uvx 3uvy 3uw9 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 3x1u 3x1v 4gqb 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4m38 4n3w 4n4f 4qut 4quu 4qyd 4u9w 4ym5 4ym6 4yy6 4yyd 4yyg 4yyh 4yyi 4yyj 4yyk 4yym 4yyn 4z2m 4z5t 5av5 5av6 5av8 5av9 5avb 5avc 5ay8 5b0y 5b0z 5b24 5b2i 5b2j 5b31 5b32 5b33 5b40 5bnv 5bnx 5bo0 5c3i 5cpi 5cpj 5cpk 5fa5 5ffw 5fwe 5gse 5gsu 5gt0 5gt3 5gtc 5gxq 5ja4 5jrg 5kdm 5teg 5x7x
        TP53B_HUMAN | Q128881gzh 1kzy 1xni 2g3r 2ig0 2mwo 2mwp 3lgf 3lgl 3lh0 4cri 4rg2 4x34 5ecg 5j26 5kgf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2LVM)