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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF ANTI-HIV-1 V3-FAB F425-B4E8 IN COMPLEX WITH A V3-PEPTIDE
 
Authors :  C. H. Bell, A. Schiefner, R. L. Stanfield, I. A. Wilson
Date :  30 Jul 07  (Deposition) - 15 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Fab-Peptide Complex, Hiv-1, Gp120, V3 Loop, Immunoglobulin Fold, Aids, Apoptosis, Envelope Protein, Fusion Protein, Glycoprotein, Host-Virus Interaction, Membrane, Transmembrane, Viral Immunoevasion, Virion, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. H. Bell, R. Pantophlet, A. Schiefner, L. A. Cavacini, R. L. Stanfield, D. R. Burton, I. A. Wilson
Structure Of Antibody F425-B4E8 In Complex With A V3 Peptid Reveals A New Binding Mode For Hiv-1 Neutralization.
J. Mol. Biol. V. 375 969 2008
PubMed-ID: 18068724  |  Reference-DOI: 10.1016/J.JMB.2007.11.013

(-) Compounds

Molecule 1 - FAB F425-B4E8, LIGHT CHAIN
    ChainsL
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHMMA MYELOMA CELLS
    Expression System CommonHUMAN
    Expression System Taxid9606
    FragmentLIGHT CHAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - FAB F425-B4E8, HEAVY CHAIN
    ChainsH
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHMMA MYELOMA CELLS
    Expression System CommonHUMAN
    Expression System Taxid9606
    FragmentHEAVY CHAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - ENVELOPE GLYCOPROTEIN GP120
    ChainsP
    EngineeredYES
    FragmentRESIDUES 301-326
    Other DetailsTHIS SEQUENCE OCCURS IN HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (ISOLATE MN)
    SynonymENV POLYPROTEIN
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CL4Ligand/IonCHLORIDE ION
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN4Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN H:28 , SER H:31 , NAG H:228BINDING SITE FOR RESIDUE NAG H 227
02AC3SOFTWARENAG H:227 , BMA H:229BINDING SITE FOR RESIDUE NAG H 228
03AC4SOFTWARENAG H:228BINDING SITE FOR RESIDUE BMA H 229
04AC5SOFTWAREHIS H:172 , THR H:192 , ASN L:137 , ASN L:138 , CL L:217BINDING SITE FOR RESIDUE ZN L 215
05AC6SOFTWAREGLN L:24 , HIS L:70 , HOH L:219BINDING SITE FOR RESIDUE ZN L 216
06AC7SOFTWAREASN L:138 , ZN L:215BINDING SITE FOR RESIDUE CL L 217
07AC8SOFTWAREASP H:53 , GLU H:55 , CL H:234BINDING SITE FOR RESIDUE ZN H 230
08AC9SOFTWAREGLU H:85 , CL H:232 , CL H:233 , GLU L:81BINDING SITE FOR RESIDUE ZN H 231
09AD1SOFTWAREZN H:231 , GLU L:81BINDING SITE FOR RESIDUE CL H 232
10BC1SOFTWARETHR H:84 , ZN H:231 , GLU L:81BINDING SITE FOR RESIDUE CL H 233
11BC2SOFTWARESER H:52 , ASP H:53 , THR H:56 , ZN H:230BINDING SITE FOR RESIDUE CL H 234

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194
5L:214 -H:127

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:140 -Pro L:141
3Phe H:148 -Pro H:149
4Glu H:150 -Pro H:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_066403W41RIGKC_HUMANDisease (IGKCD)  ---LW148R
2UniProtVAR_003897V84LIGKC_HUMANPolymorphism  ---LV191L

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGKC_HUMAN85-91  1L:192-198

(-) Exons   (0, 0)

(no "Exon" information available for 2QSC)

(-) 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 H from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qscH01 H:1-113 Immunoglobulins                                                                                            2qscH02 H:114-226 Immunoglobulins                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeeee....eeeeeee...eeeee........eeeee.....eeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeee......eeeeeeehhhheeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qsc H    1 QVQLVQSGGGLVQPGGSLRLSCAAFGFNFSSYVMHWVRQAPGQGLEYLSAISSDGETTYHANSVKGRFTSSRDNSKNTLFLQMGSLRTEDVAVYYCARDRYYETSGSNAFDVWGQGTMVVVSSASTKGPSVFPLAPCTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSTQTYTCNVDHKPSNTKVDKTVE  226
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F       110       120      |139       149    |||164    || 175    || 186       200||     213       223|
                                                                              52A                            82A||               100A|||||                        127|              154|||    169|      180|          195|||               223|
                                                                                                              82B|                100B||||                         137               156||     171       182           200||                226
                                                                                                               82C                 100C|||                                            157|                              203|                   
                                                                                                                                    100D||                                             162                               205                   
                                                                                                                                     100E|                                                                                                     
                                                                                                                                      100F                                                                                                     

Chain L from PDB  Type:PROTEIN  Length:215
 aligned with IGKC_HUMAN | P01834 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:215
                                                                                                                                        1                                                                                                          
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102     
          IGKC_HUMAN      - ------------------------------------------------------------------------------------------------------------RTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  107
               SCOP domains --d2qscl1 L:3-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                d2qscl2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 2qscL01 L:1-107 Immunoglobulins                                                                             2qscL02 L:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------L----------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qsc L    1 NSVLTQSPSSLSASVGDRVTITCQASQDISNYLNWYQHKPGKAPKLLIYTASNLETGVPSRFSGGGSGTHFSFTITSLQPEDAATYFCQQYDNLGDLSFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90     |  99       109       119       129       139       149       159       169       179       189       199       209     
                                                                                                                         95A                                                                                                                       

Chain P from PDB  Type:PROTEIN  Length:15
 aligned with ENV_HV1MN | P05877 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:15
                                   318     
           ENV_HV1MN    309 RKRIHIGPGRAFYTT  323
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains GP120-2qscP01   Pfam domains
         Sec.struct. author .eeee......eeee Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                2qsc P  304 RKRIHIGPGRAFYTT  320
                                 ||315     
                               309|        
                                312        

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (48, 67)

Asymmetric/Biological Unit(hide GO term definitions)
Chain L   (IGKC_HUMAN | P01834)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
    GO:0034987    immunoglobulin receptor binding    Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
    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).
biological process
    GO:0050853    B cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0038096    Fc-gamma receptor signaling pathway involved in phagocytosis    An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
    GO:0006956    complement activation    Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
    GO:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0006911    phagocytosis, engulfment    The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
    GO:0006910    phagocytosis, recognition    The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
    GO:0050871    positive regulation of B cell activation    Any process that activates or increases the frequency, rate or extent of B cell activation.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0001895    retina homeostasis    A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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:0042571    immunoglobulin complex, circulating    An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
    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.

Chain P   (ENV_HV1MN | P05877)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019082    viral protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0044175    host cell endosome membrane    The lipid bilayer surrounding a host cell endosome.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1MN | P058771acy 1ai1 1f58 1ggi 1k5m 1nak 1niz 1nj0 1q1j 2b0s 3e6h 3go1 3mlw 3mlx 3uji 4m1d 4xaw 4xbe 4xc1 4xc3 4xcf 4xmk
        IGHG2_HUMAN | P018594haf 4hag 4l4j
        IGKC_HUMAN | P018341a4j 1a4k 1cly 1d5b 1d5i 1d6v 1dfb 1gaf 1hez 1hkl 1hzh 1i7z 1mim 1n0x 1om3 1op3 1op5 1ucb 2ny7 2o5x 2o5y 2o5z 2qqk 2qql 2qqn 2r56 2rfx 2vxq 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3cfj 3cfk 3csy 3d0l 3d85 3dvg 3dvn 3eyf 3eyo 3eyq 3iu3 3o11 3qct 3qcu 3qcv 3ru8 3u0w 3u7w 3u7y 3vh8 3wuw 3x11 3x12 4d3c 4d9r 4hix 4nm4 4nm8 4xmp 4xny 4xnz 4xxd 4ydv 5b38 5b39 5c7k 5esv 5esz 5ewi 5veb 5viy

(-) Related Entries Specified in the PDB File

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