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(-) Description

Title :  SUBSTITUTED 2-NAPHTHAMIDINE INHIBITORS OF UROKINASE
 
Authors :  M. D. Wendt, A. Geyer, W. J. Mcclellan, T. W. Rockway, M. Weitzberg, X. Zhao, R. Mantei, K. Stewart, V. Nienaber, V. Klinghofer, V. L. Giranda
Date :  19 Mar 04  (Deposition) - 27 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A
Keywords :  Plasminogen Activation, Hydrolase, Serine Protease, Glycoprotein, Kringle, Egf-Like Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. D. Wendt, A. Geyer, W. J. Mcclellan, T. W. Rockway, M. Weitzberg, X. Zhao, R. Mantei, K. Stewart, V. Nienaber, V. Klinghofer, V. L. Giranda
Interaction With The S1Beta-Pocket Of Urokinase: 8-Heterocycle Substituted And 6, 8-Disubstituted 2-Naphthamidine Urokinase Inhibitors.
Bioorg. Med. Chem. Lett. V. 14 3063 2004
PubMed-ID: 15149645
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UROKINASE-TYPE PLASMINOGEN ACTIVATOR
    ChainsA
    EC Number3.4.21.73
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    GenePLAU
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUPA, U-PLASMINOGEN ACTIVATOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2UI21Ligand/Ion8-(PYRIMIDIN-2-YLAMINO)NAPHTHALENE-2-CARBOXIMIDAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:61 , HIS A:107 , THR A:191 , LYS A:193 , MET A:194 , HOH A:1073BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREHIS A:54 , GLN A:208 , GLY A:209 , SER A:211 , UI2 A:1001BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWARETYR A:138 , ARG A:246 , HIS A:249BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWAREASN A:11 , SER A:157 , ASP A:205 , SER A:206 , CYS A:207 , GLN A:208 , SER A:211 , VAL A:229 , GLY A:232 , GLY A:234 , CYS A:235 , GLY A:242 , SO4 A:302BINDING SITE FOR RESIDUE UI2 A 1001

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:34 -A:55
2A:46 -A:122
3A:147 -A:217
4A:180 -A:196
5A:207 -A:235

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038731K231QUROK_HUMANPolymorphism2227567AK61Q

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.UROK_HUMAN179-424  1A:1-258
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.UROK_HUMAN220-225  1A:50-55
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.UROK_HUMAN370-381  1A:205-216

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3cENST000003727643cENSE00001820360chr10:75670915-7567097662UROK_HUMAN-00--
1.4bENST000003727644bENSE00002193721chr10:75671283-7567137088UROK_HUMAN1-19190--
1.5ENST000003727645ENSE00001276413chr10:75671799-7567182628UROK_HUMAN20-29100--
1.6aENST000003727646aENSE00001169210chr10:75671973-75672080108UROK_HUMAN29-65370--
1.7bENST000003727647bENSE00001169200chr10:75672682-75672856175UROK_HUMAN65-123590--
1.8ENST000003727648ENSE00000834105chr10:75673048-7567313992UROK_HUMAN123-154320--
1.9bENST000003727649bENSE00001169184chr10:75673297-75673516220UROK_HUMAN154-227741A:1-57 (gaps)57
1.10ENST0000037276410ENSE00001169178chr10:75673738-75673886149UROK_HUMAN227-277511A:57-111 (gaps)55
1.11ENST0000037276411ENSE00001169173chr10:75674534-75674674141UROK_HUMAN277-324481A:111-15848
1.13ENST0000037276413ENSE00001169164chr10:75675009-75675157149UROK_HUMAN324-373501A:158-208 (gaps)51
1.14dENST0000037276414dENSE00001892698chr10:75676147-756772551109UROK_HUMAN374-431581A:209-25850

(-) 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:245
 aligned with UROK_HUMAN | P00749 from UniProtKB/Swiss-Prot  Length:431

    Alignment length:246
                                                              214                                                                                                                                                                                                                 
                                                            213 |                                                                                                                                                                                                                 
                                   188       198       208    | |217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417      
           UROK_HUMAN   179 IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSL-ISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTICLPSMYNDPQFGTSCEITGFGKENSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHT 423
               SCOP domains d1sqoa_ A: Urokinase-type plasminoge n activator (LMW U-PA), catalytic domain                                                                                                                                                                          SCOP domains
               CATH domains 1sqoA01     1sqoA02 A:13-131,A:249-2 58 Trypsin-like serine proteases                                                   1sqoA01 A:1-12,A:132-248 Trypsin-like serine proteases                                                              1sqoA02    CATH domains
               Pfam domains Trypsin-1sqoA01 A:1-254                                                                                                                                                                                                                           ---- Pfam domains
         Sec.struct. author ....ee.hhhhh..eeeeeee.....eeeeeeeeee-e..eeeehhhhh....hhh.eeeee............eeeeeeeeee....ee....ee...eeeeee.............................eeeeee...............eeeeeeeehhhhhh....hhhhh...eeeee...............eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------Q------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:1-258 UniProt: 179-424                                                                                                                                                                                                             PROSITE (1)
                PROSITE (2) ------------------------------------------TRYPSI------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------ PROSITE (2)
           Transcript 1 (1) -------------------------------------------------Exon 1.10  PDB: A:57-111 (gaps) UniProt: 227-277   ----------------------------------------------Exon 1.13  PDB: A:158-208 (gaps) UniProt: 324-373 Exon 1.14d  PDB: A:209-258 UniProt: 374-431        Transcript 1 (1)
           Transcript 1 (2) Exon 1.9b  PDB: A:1-57 (gaps) UniProt: 154-227    -------------------------------------------------Exon 1.11  PDB: A:111-158 UniProt: 277-324      --------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1sqo A   1 IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLM-SPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTICLPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHT 258
                                    10        20  |||   32||  || |46|       57     |||69    ||| 81        91       101       111       121       131       141       151       161   ||  172       182       192       202       212       222       232       242       252      
                                                 23||   32|| 39| ||||             63||     74||                                                                                    165|                                                                                           
                                                  25|    34|  41 ||||              65|      76|                                                                                     167                                                                                           
                                                   27     36    43|||               67       78                                                                                                                                                                                   
                                                                 44||                                                                                                                                                                                                             
                                                                  46|                                                                                                                                                                                                             
                                                                   48                                                                                                                                                                                                             

   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  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (48, 48)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UROK_HUMAN | P00749)
molecular function
    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).
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0071498    cellular response to fluid shear stress    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 fluid shear stress stimulus. Fluid shear stress is the force acting on an object in a system where the fluid is moving across a solid surface.
    GO:0071333    cellular response to glucose 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 glucose stimulus.
    GO:0035729    cellular response to hepatocyte growth factor 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 hepatocyte growth factor stimulus.
    GO:0071456    cellular response to hypoxia    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 lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0071222    cellular response to lipopolysaccharide    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 lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0071310    cellular response to organic substance    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 an organic substance stimulus.
    GO:0072734    cellular response to staurosporine    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 staurosporine stimulus.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0007566    embryo implantation    Attachment of the blastocyst to the uterine lining.
    GO:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0070997    neuron death    The process of cell death in a neuron.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0060279    positive regulation of ovulation    Any process that activates or increases the frequency, rate or extent of ovulation, the release of a mature ovum/oocyte from an ovary.
    GO:2000379    positive regulation of reactive oxygen species metabolic process    Any process that activates or increases the frequency, rate or extent of reactive oxygen species metabolic process.
    GO:0014911    positive regulation of smooth muscle cell migration    Any process that activates, maintains or increases the frequency, rate or extent of smooth muscle cell migration.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0033628    regulation of cell adhesion mediated by integrin    Any process that modulates the frequency, rate, or extent of cell adhesion mediated by integrin.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:2000345    regulation of hepatocyte proliferation    Any process that modulates the frequency, rate or extent of hepatocyte proliferation.
    GO:0010469    regulation of receptor activity    Any process that modulates the frequency, rate or extent of receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0014910    regulation of smooth muscle cell migration    Any process that modulates the frequency, rate or extent of smooth muscle cell migration.
    GO:2000097    regulation of smooth muscle cell-matrix adhesion    Any process that modulates the frequency, rate or extent of smooth muscle cell-matrix adhesion.
    GO:0061041    regulation of wound healing    Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
    GO:0014823    response to activity    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an activity stimulus.
    GO:0035728    response to hepatocyte growth factor    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hepatocyte growth factor stimulus.
    GO:0055093    response to hyperoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating increased oxygen tension.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0043403    skeletal muscle tissue regeneration    The regrowth of skeletal muscle tissue to repair injured or damaged muscle fibers in the postnatal stage.
    GO:0014909    smooth muscle cell migration    The orderly movement of a smooth muscle cell from one site to another, often during the development of a multicellular organism.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UROK_HUMAN | P007491c5w 1c5x 1c5y 1c5z 1ejn 1f5k 1f5l 1f92 1fv9 1gi7 1gi8 1gi9 1gj7 1gj8 1gj9 1gja 1gjb 1gjc 1gjd 1kdu 1lmw 1o3p 1o5a 1o5b 1o5c 1owd 1owe 1owh 1owi 1owj 1owk 1sc8 1sqa 1sqt 1u6q 1urk 1vj9 1vja 1w0z 1w10 1w11 1w12 1w13 1w14 2fd6 2i9a 2i9b 2nwn 2o8t 2o8u 2o8w 2r2w 2vin 2vio 2vip 2viq 2viv 2viw 2vnt 3bt1 3bt2 3ig6 3kgp 3khv 3kid 3m61 3mhw 3mwi 3ox7 3oy5 3oy6 3pb1 3qn7 3u73 4dva 4dw2 4fu7 4fu8 4fu9 4fub 4fuc 4fud 4fue 4fuf 4fug 4fuh 4fui 4fuj 4gly 4h42 4jk5 4jk6 4jni 4jnl 4k24 4mnv 4mnw 4mnx 4mny 4os1 4os2 4os4 4os5 4os6 4os7 4x0w 4x1n 4x1p 4x1q 4x1r 4x1s 4xsk 4zhl 4zhm 4zkn 4zko 4zkr 4zks 5hgg

(-) Related Entries Specified in the PDB File

1owd 1owe 1owh 1owi 1owj 1owk 1sqa 1sqt