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(-) Description

Title :  BACE1 WITH THE AMINOHYDANTOIN COMPOUND R-58
 
Authors :  A. M. Olland, R. Chopra
Date :  12 Aug 09  (Deposition) - 02 Mar 10  (Release) - 02 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Bace1, Xray, Inhibitor, Alternative Splicing, Aspartyl Protease, Disulfide Bond, Glycoprotein, Hydrolase, Membrane, Polymorphism, Protease, Transmembrane, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. S. Malamas, J. Erdei, I. Gunawan, J. Turner, Y. Hu, E. Wagner, K. Fan, R. Chopra, A. Olland, J. Bard, S. Jacobsen, R. L. Magolda, M. Pangalos, A. J. Robichaud
Design And Synthesis Of 5, 5'-Disubstituted Aminohydantoins As Potent And Selective Human Beta-Secretase (Bace1) Inhibitors.
J. Med. Chem. V. 53 1146 2010
PubMed-ID: 19968289  |  Reference-DOI: 10.1021/JM901414E

(-) Compounds

Molecule 1 - BETA-SECRETASE 1
    ChainsA
    EC Number3.4.23.46
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCATALYTIC DOMAIN
    GeneBACE1, BACE, KIAA1149
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 1, BETA-SITE APP CLEAVING ENZYME 1, MEMBRANE- ASSOCIATED ASPARTIC PROTEASE 2, MEMAPSIN-2, ASPARTYL PROTEASE 2, ASP 2, ASP2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
15691Ligand/Ion(5R)-2-AMINO-5-(4-FLUORO-3-PYRIMIDIN-5-YLPHENYL)-3-METHYL-5-[4-(TRIFLUOROMETHOXY)PHENYL]-3,5-DIHYDRO-4H-IMIDAZOL-4-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:11 , GLY A:73 , GLN A:74 , GLY A:75 , ASP A:94 , SER A:97 , VAL A:131 , TRP A:138 , PHE A:170 , ILE A:172 , TRP A:177 , ILE A:180 , ARG A:190 , ASP A:290 , GLY A:292 , THR A:293 , THR A:294 , HOH A:474 , HOH A:490BINDING SITE FOR RESIDUE 569 A 1

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:217 -A:421
2A:279 -A:444
3A:331 -A:381

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:84 -Pro A:85
2Arg A:190 -Pro A:191
3Tyr A:284 -Asp A:285
4Gly A:434 -Pro A:435

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_060692V265ABACE1_HUMANPolymorphism28989503AV266A

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.BACE1_HUMAN75-416  1A:76-417
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.BACE1_HUMAN90-101  1A:91-102

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003130051bENSE00002169377chr11:117186972-117186251722BACE1_HUMAN1-87871A:60-8829
1.2dENST000003130052dENSE00001779698chr11:117167677-11716758989BACE1_HUMAN88-117301A:89-11830
1.4cENST000003130054cENSE00001602221chr11:117166063-117165847217BACE1_HUMAN117-189731A:118-190 (gaps)73
1.5bENST000003130055bENSE00001732292chr11:117164724-117164587138BACE1_HUMAN190-235461A:191-236 (gaps)46
1.6bENST000003130056bENSE00001231658chr11:117163904-117163770135BACE1_HUMAN236-280451A:237-28145
1.7cENST000003130057cENSE00001053358chr11:117162529-117162428102BACE1_HUMAN281-314341A:282-31534
1.8bENST000003130058bENSE00001053366chr11:117161765-117161616150BACE1_HUMAN315-364501A:316-36550
1.9dENST000003130059dENSE00001385289chr11:117161375-117161204172BACE1_HUMAN365-422581A:366-423 (gaps)58
1.10fENST0000031300510fENSE00002041784chr11:117160523-1171564024122BACE1_HUMAN422-501801A:423-448 (gaps)26

(-) 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:366
 aligned with BACE1_HUMAN | P56817 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:389
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438         
          BACE1_HUMAN    59 SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI 447
               SCOP domains d3inha_ A: beta-secretase (memapsin)                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------3inhA01 A:76-208 Acid Proteases                                                                                                      3inhA02 A:209       -448 Acid Proteases                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eeee....eeeeeee....eeeeeeee.....eeee...........hhhhh...eeeeeeeee..---.eeeeeeeeeee........eeeeeeeeeee...........eeee..hhhhh.......hhhhhhhhhh.....eeeee.....-------..eeeeeeee...hhh.eeeeeeeee.......ee.eeeeee..ee...hhhhhhh..eee......eeeehhhhhhhhhhhhhhh.....hhhhhh............hhhhh..eeeeee.....eeeeeeehhhhhee.----------..ee.eeee...eeehhhhhh.eeeeeehhh.eeeeeee...........eeeeeee..---...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------PEPTIDASE_A1  PDB: A:76-417 UniProt: 75-416                                                                                                                                                                                                                                                                                                           ------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------ASP_PROTEASE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1b  PDB: A:60-88      Exon 1.2d  PDB: A:89-118      ------------------------------------------------------------------------Exon 1.5b  PDB: A:191-236 (gaps)              Exon 1.6b  PDB: A:237-281 UniProt: 236-280   Exon 1.7c  PDB: A:282-315         Exon 1.8b  PDB: A:316-365 UniProt: 315-364        ---------------------------------------------------------Exon 1.10f [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.4c  PDB: A:118-190 (gaps) UniProt: 117-189                        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9d  PDB: A:366-423 (gaps) UniProt: 365-422         ------------------------- Transcript 1 (2)
                 3inh A  60 SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPY---KWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGF-------LASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRP----------CYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTL---DCGYNI 448
                                    69        79        89        99       109       119       129   |   139       149       159       169       179       189       199       209       219 |     229       239       249       259       269       279       289       299       309       319       329       339       349       359       369|        - |     389       399       409       419       429       439   |     
                                                                                                   133 137                                                                                 221     229                                                                                                                                          370        381                                                       439 443     

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BACE1_HUMAN | P56817)
molecular function
    GO:0001540    amyloid-beta binding    Interacting selectively and non-covalently with amyloid-beta peptide/protein and/or its precursor.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0008798    beta-aspartyl-peptidase activity    Catalysis of the cleavage of a beta-linked aspartic residue from the N-terminus of a polypeptide.
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0050435    amyloid-beta metabolic process    The chemical reactions and pathways involving amyloid-beta, a glycoprotein associated with Alzheimer's disease, and its precursor, amyloid precursor protein (APP).
    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:0006509    membrane protein ectodomain proteolysis    The proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain).
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0070931    Golgi-associated vesicle lumen    The volume enclosed by the membrane of a Golgi-associated vesicle.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005771    multivesicular body    A type of endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BACE1_HUMAN | P568171fkn 1m4h 1py1 1sgz 1tqf 1ujj 1ujk 1w50 1w51 1xn2 1xn3 1xs7 1ym2 1ym4 2b8l 2b8v 2f3e 2f3f 2fdp 2g94 2hiz 2hm1 2iqg 2irz 2is0 2ntr 2oah 2of0 2ohk 2ohl 2ohm 2ohn 2ohp 2ohq 2ohr 2ohs 2oht 2ohu 2p4j 2p83 2p8h 2ph6 2ph8 2q11 2q15 2qk5 2qmd 2qmf 2qmg 2qp8 2qu2 2qu3 2qzk 2qzl 2va5 2va6 2va7 2vie 2vij 2viy 2viz 2vj6 2vj7 2vj9 2vkm 2vnm 2vnn 2wez 2wf0 2wf1 2wf2 2wf3 2wf4 2wjo 2xfi 2xfj 2xfk 2zdz 2ze1 2zhr 2zhs 2zht 2zhu 2zhv 2zjh 2zji 2zjj 2zjk 2zjl 2zjm 2zjn 3bra 3buf 3bug 3buh 3cib 3cic 3cid 3ckp 3ckr 3dm6 3duy 3dv1 3dv5 3exo 3fkt 3h0b 3hvg 3hw1 3i25 3igb 3in3 3in4 3ind 3ine 3inf 3ivh 3ivi 3ixj 3ixk 3k5c 3k5d 3k5f 3k5g 3kmx 3kmy 3kn0 3kyr 3l38 3l3a 3l58 3l59 3l5b 3l5c 3l5d 3l5e 3l5f 3lhg 3lnk 3lpi 3lpj 3lpk 3msj 3msk 3msl 3n4l 3nsh 3ohf 3ohh 3ooz 3pi5 3qbh 3qi1 3r1g 3r2f 3rsv 3rsx 3rth 3rtm 3rtn 3ru1 3rvi 3s2o 3s7l 3s7m 3skf 3skg 3tpj 3tpl 3tpp 3tpr 3u6a 3udh 3udj 3udk 3udm 3udn 3udp 3udq 3udr 3udy 3ufl 3uqp 3uqr 3uqu 3uqw 3uqx 3veu 3vf3 3vg1 3vv6 3vv7 3vv8 3wb4 3wb5 3zmg 3zov 4acu 4acx 4azy 4b00 4b05 4b0q 4b1c 4b1d 4b1e 4b70 4b72 4b77 4b78 4bek 4bfd 4d83 4d85 4d88 4d89 4d8c 4dh6 4di2 4dju 4djv 4djw 4djx 4djy 4dpf 4dpi 4dus 4dv9 4dvf 4ewo 4exg 4fco 4fgx 4fm7 4fm8 4fri 4frj 4frk 4frs 4fs4 4fse 4fsl 4gid 4gmi 4h1e 4h3f 4h3g 4h3i 4h3j 4ha5 4hzt 4i0d 4i0e 4i0f 4i0g 4i0h 4i0i 4i0j 4i0z 4i10 4i11 4i12 4i1c 4ivs 4ivt 4j0p 4j0t 4j0v 4j0y 4j0z 4j17 4j1c 4j1e 4j1f 4j1h 4j1i 4j1k 4joo 4jp9 4jpc 4jpe 4k8s 4k9h 4ke0 4ke1 4l7g 4l7h 4l7j 4lc7 4lxa 4lxk 4lxm 4n00 4pzw 4pzx 4r5n 4r8y 4r91 4r92 4r93 4r95 4rcd 4rce 4rcf 4rrn 4rro 4rrs 4trw 4try 4trz 4wtu 4wy1 4wy6 4x2l 4x7i 4xkx 4xxs 4ybi 4zpe 4zpf 4zpg 4zsm 4zsp 4zsq 4zsr 5clm 5dqc 5enk 5enm 5ezx 5ezz 5f00 5f01 5hd0 5hdu 5hdv 5hdx 5hdz 5he4 5he5 5he7 5htz 5hu0 5hu1 5i3v 5i3w 5i3x 5i3y 5ie1 5kqf 5kr8 5t1u 5t1w 5tol 5uyu 5v0n

(-) Related Entries Specified in the PDB File

3ind 3ine 3inf