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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-IL-15 ANTIBODY IN COMPLEX WITH HUMAN IL-15
 
Authors :  D. C. Lowe, S. Gerhardt, A. Ward, D. Hargreaves, M. Anderson, S. Stgalla K. Vousden, F. Ferraro, R. A. Pauptit, D. Cochrane, D. V. Pattison, C. B B. Popovic, D. K. Finch, T. Wilkinson, M. Sleeman, T. J. Vaughan, S. Cru P. R. Mallinder
Date :  01 Sep 10  (Deposition) - 29 Dec 10  (Release) - 06 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Immune System, Affinity Maturation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. C. Lowe, S. Gerhardt, A. Ward, D. Hargreaves, M. Anderson, F. Ferraro, R. A. Pauptit, D. V. Pattison, C. Buchanan, B. Popovic, D. K. Finch, T. Wilkinson, M. Sleeman, T. J. Vaughan, P. R. Mallinder
Engineering A High Affinity Anti-Il-15 Antibody: Crystal Structure Reveals An Alpha-Helix In Vh Cdr3 As Key Component Of Paratope.
J. Mol. Biol. V. 406 160 2011
PubMed-ID: 21167836  |  Reference-DOI: 10.1016/J.JMB.2010.12.017

(-) Compounds

Molecule 1 - INTERLEUKIN 15
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPT7#3.3
    Expression System StrainBL21(DE3)STAR
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - ANTI-IL-15 ANTIBODY
    ChainsH
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293/EBNA
    Expression System CommonHUMAN
    Expression System Taxid9606
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - ANTI-IL-15 ANTIBODY
    ChainsL
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293/EBNA .
    Expression System CommonHUMAN
    Expression System Taxid9606
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER H:25 , ASN H:54 , GLY H:55 , THR H:71 , HOH H:2044 , HOH H:2045BINDING SITE FOR RESIDUE SO4 H1216
2AC2SOFTWARELYS A:41 , TRP H:99 , PRO H:100 , LEU H:100A , HOH H:2046BINDING SITE FOR RESIDUE SO4 H1217
3AC3SOFTWAREARG L:52 , ARG L:54 , SER L:63BINDING SITE FOR RESIDUE SO4 L1210

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:35 -A:85
2A:42 -A:88
3H:22 -H:92
4H:140 -H:196
5L:23 -L:88
6L:134 -L:193

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Asp H:101 -Pro H:102
2Thr H:131 -Ser H:132
3Phe H:146 -Pro H:147
4Glu H:148 -Pro H:149
5Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XQB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XQB)

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003206501aENSE00001517654chr4:142557752-142557901150IL15_HUMAN-00--
1.2ENST000003206502ENSE00001191128chr4:142577339-142577460122IL15_HUMAN-00--
1.5cENST000003206505cENSE00001342283chr4:142640519-142640629111IL15_HUMAN1-440--
1.6aENST000003206506aENSE00001081769chr4:142641622-14264171998IL15_HUMAN5-37330--
1.8bENST000003206508bENSE00001081768chr4:142643077-14264316185IL15_HUMAN37-65291A:1-1717
1.9ENST000003206509ENSE00001081766chr4:142649093-14264913745IL15_HUMAN66-80151A:21-3212
1.10ENST0000032065010ENSE00001081765chr4:142651000-142651137138IL15_HUMAN81-126461A:33-7543
1.11cENST0000032065011cENSE00001911998chr4:142653891-142654588698IL15_HUMAN127-162361A:81-11333

(-) 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:105
 aligned with IL15_HUMAN | P40933 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:113
                                    58        68        78        88        98       108       118       128       138       148       158   
          IL15_HUMAN     49 NWVNVISDLKKIEDLIQSMHIDATLYTESDVHPSCKVTAMKCFLLELQVISLESGDASIHDTVENLIILANNSLSSNGNVTESGCKECEELEEKNIKEFLQSFVHIVQMFINT  161
               SCOP domains d2xqba_ A: automa   ted matches                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains IL15-2xqbA01 A:1-   112                                                                                         - Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.---....eee....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh-----......hhhhheeehhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.8b        Exon 1.9       Exon 1.10  PDB: A:33-75 UniProt: 81-126       Exon 1.11c  PDB: A:81-113           Transcript 1
                2xqb A    1 NWVNVISDLKKIEDLIQ---IDATLYTESDVHPSCKVTAMKCFLLELQVISLESGDASIHDTVENLIILANNSLS-----TESGCKECEELEEKNIKEFLQSFVHIVQMFINT  113
                                    10      |  -|       30        40        50        60        70    |    -|       90       100       110   
                                           17  21                                                    75    81                                

Chain H from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhh.eeeeeee.....eeeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeee...hhhhhhhh........eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh...eeee...ee.....eeeeeeeeee........eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xqb H    1 QVQLVQSGAEVKKPGASVKVSCKASGYSFSSFGISWVRQAPGQGLEWLGWISAFNGYTKYAQKFQDRVTMTTDTSTSTAYMELRSLRSDDTAVYYCARDPAAWPLQQSLAWFDPWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||     108       118       128       138       148       158       168       178       188       198       208       
                                                                              52A                            82A||               100A|||||||                                                                                                                   
                                                                                                              82B|                100B||||||                                                                                                                   
                                                                                                               82C                 100C|||||                                                                                                                   
                                                                                                                                    100D||||                                                                                                                   
                                                                                                                                     100E|||                                                                                                                   
                                                                                                                                      100F||                                                                                                                   
                                                                                                                                       100G|                                                                                                                   
                                                                                                                                        100H                                                                                                                   

Chain L from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                           
               SCOP domains d2xqbl1 L:5-107 automated matches                                                                    d2xqbl2 L:108-209 automated matches                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.....eeeeee.....eeeeee......eeee.............eeeee...eeeeee...hhhhheeeeeeeee....eeee...eeeee.......eeeee..hhhhhh...eeeeeeeeee.....eeeeee..eee...eee.........eeeeeeeeehhhhhhh...eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xqb L    5 TQPPSASGTPGQRVTISCSGSTNYVYWYQQLPGTAPKLLIYRDRRRPSGVPDRFSGSKSGTSASLAISGLRSEDEADYYCAWYDRELSEWVFGGGTKLTVLQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                                ||  15        25 ||     38        48        58        68        78        88       |96       106       116       126       136       146       156       166|      177       187       197       207  
                                9|              27|                                                              95A|                                                                    166|                                         
                                11               31                                                               95B                                                                     168                                         

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IL15_HUMAN | P40933)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0005126    cytokine receptor binding    Interacting selectively and non-covalently with a cytokine receptor.
    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:0001866    NK T cell proliferation    The expansion of a NK T cell population by cell division.
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0048469    cell maturation    A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state.
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0071305    cellular response to vitamin D    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 vitamin D stimulus.
    GO:0045062    extrathymic T cell selection    The process of T cell selection that occurs in extrathymic locations, often resulting T cells of distinct specificities from those selected in the thymus.
    GO:0030212    hyaluronan metabolic process    The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
    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:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0048535    lymph node development    The process whose specific outcome is the progression of lymph nodes over time, from their formation to the mature structure. A lymph node is a round, oval, or bean shaped structure localized in clusters along the lymphatic vessels, with a distinct internal structure including specialized vasculature and B- and T-zones for the activation of lymphocytes.
    GO:0001779    natural killer cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a natural killer cell.
    GO:0048662    negative regulation of smooth muscle cell proliferation    Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0050778    positive regulation of immune response    Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0032740    positive regulation of interleukin-17 production    Any process that activates or increases the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines.
    GO:0032825    positive regulation of natural killer cell differentiation    Any process that activates or increases the frequency, rate or extent of natural killer cell differentiation.
    GO:0032819    positive regulation of natural killer cell proliferation    Any process that activates or increases the frequency, rate or extent of natural killer cell proliferation.
    GO:1904100    positive regulation of protein O-linked glycosylation    Any process that activates or increases the frequency, rate or extent of protein O-linked glycosylation.
    GO:0034105    positive regulation of tissue remodeling    Any process that activates or increases the frequency, rate, or extent of tissue remodeling.
    GO:0045580    regulation of T cell differentiation    Any process that modulates the frequency, rate or extent of T cell differentiation.
    GO:0050691    regulation of defense response to virus by host    Any host process that modulates the frequency, rate, or extent of the antiviral response of a host cell or organism.
    GO:0031667    response to nutrient levels    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 reflecting the presence, absence, or concentration of nutrients.
    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:0014732    skeletal muscle atrophy    A process, occurring in skeletal muscle, that is characterized by a decrease in protein content, fiber diameter, force production and fatigue resistance in response to different conditions such as starvation, aging and disuse.
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:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IL15_HUMAN | P409332z3q 2z3r 4gs7

(-) Related Entries Specified in the PDB File

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