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(-) Description

Title :  CRYSTAL STRUCTURE OF THE KIFC3 MOTOR DOMAIN IN COMPLEX WITH ADP
 
Authors :  J. Wang, Y. Shen, W. Tempel, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  25 May 06  (Deposition) - 27 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinesin, Motor Domain, Adp, Structural Genomics, Structur Al Genomics Consortium, Sgc, Structural Genomics Consortium, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Wang, Y. Shen, W. Tempel, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of The Kifc3 Motor Domain In Complex With Adp
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KINESIN-LIKE PROTEIN KIFC3 VARIANT
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP28A-LIC
    Expression System StrainBL21-CODONPLUS (DE-3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Gene3801
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3UNX11Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:153 , HOH A:168 , HOH A:169 , HOH A:172 , THR A:535 , ADP A:901BINDING SITE FOR RESIDUE MG A 801
02AC2SOFTWAREHOH A:29 , HOH A:121 , HOH A:153 , HOH A:172 , HOH A:175 , ARG A:451 , ARG A:453 , PRO A:454 , THR A:456 , GLN A:529 , THR A:530 , GLY A:531 , ALA A:532 , GLY A:533 , LYS A:534 , THR A:535 , TYR A:536 , MG A:801BINDING SITE FOR RESIDUE ADP A 901
03AC3SOFTWAREGLU A:595 , ILE A:596BINDING SITE FOR RESIDUE UNX A 401
04AC4SOFTWAREMET A:538 , ASN A:548BINDING SITE FOR RESIDUE UNX A 402
05AC5SOFTWAREGLU A:613 , ASN A:639BINDING SITE FOR RESIDUE UNX A 403
06AC6SOFTWAREHOH A:89 , SER A:644 , SER A:645BINDING SITE FOR RESIDUE UNX A 404
07AC7SOFTWAREVAL A:608 , LEU A:611BINDING SITE FOR RESIDUE UNX A 405
08AC8SOFTWAREHOH A:87 , HOH A:112 , HOH A:173 , GLY A:519 , ASN A:521 , THR A:667BINDING SITE FOR RESIDUE UNX A 406
09AC9SOFTWAREARG A:692 , HIS A:696 , HIS A:717BINDING SITE FOR RESIDUE UNX A 407
10BC1SOFTWAREHOH A:57 , GLU A:589BINDING SITE FOR RESIDUE UNX A 408
11BC2SOFTWAREHOH A:26 , HOH A:184 , SER A:644 , SER A:647BINDING SITE FOR RESIDUE UNX A 409
12BC3SOFTWAREASP A:472 , HIS A:480BINDING SITE FOR RESIDUE UNX A 410
13BC4SOFTWARETHR A:612 , GLU A:613BINDING SITE FOR RESIDUE UNX A 411

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H58)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:589 -Pro A:590

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H58)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.KIFC3_HUMAN445-768  1A:445-766
2KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.KIFC3_HUMAN668-679  1A:668-679

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003796551bENSE00001928684chr16:57836435-57836282154KIFC3_HUMAN-00--
1.2ENST000003796552ENSE00001482032chr16:57832194-57831984211KIFC3_HUMAN1-58580--
1.4ENST000003796554ENSE00001662862chr16:57829053-57828911143KIFC3_HUMAN58-105480--
1.6ENST000003796556ENSE00001680881chr16:57806200-5780613566KIFC3_HUMAN106-127220--
1.7ENST000003796557ENSE00001643977chr16:57805598-57805455144KIFC3_HUMAN128-175480--
1.8ENST000003796558ENSE00000945365chr16:57805349-57805110240KIFC3_HUMAN176-255800--
1.9ENST000003796559ENSE00000945366chr16:57804612-57804439174KIFC3_HUMAN256-313580--
1.10ENST0000037965510ENSE00000945367chr16:57803867-57803720148KIFC3_HUMAN314-363500--
1.11ENST0000037965511ENSE00000945368chr16:57803637-57803507131KIFC3_HUMAN363-406440--
1.12ENST0000037965512ENSE00000945369chr16:57800897-57800786112KIFC3_HUMAN407-444380--
1.13ENST0000037965513ENSE00000945370chr16:57799552-57799371182KIFC3_HUMAN444-504611A:445-50460
1.14ENST0000037965514ENSE00000945371chr16:57798159-57798055105KIFC3_HUMAN505-539351A:505-53935
1.15ENST0000037965515ENSE00000945372chr16:57796182-57796052131KIFC3_HUMAN540-583441A:540-58344
1.16ENST0000037965516ENSE00000945373chr16:57795448-57795325124KIFC3_HUMAN583-624421A:583-62442
1.17ENST0000037965517ENSE00000945374chr16:57795083-57794954130KIFC3_HUMAN625-668441A:625-66844
1.18ENST0000037965518ENSE00000945375chr16:57794867-57794638230KIFC3_HUMAN668-744771A:668-744 (gaps)77
1.19ENST0000037965519ENSE00000945376chr16:57794328-57794194135KIFC3_HUMAN745-789451A:745-76622
1.20ENST0000037965520ENSE00000945377chr16:57793748-57793640109KIFC3_HUMAN790-826370--
1.22bENST0000037965522bENSE00001270159chr16:57792821-57792129693KIFC3_HUMAN826-83380--

(-) 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:316
 aligned with KIFC3_HUMAN | Q9BVG8 from UniProtKB/Swiss-Prot  Length:833

    Alignment length:322
                                   454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764  
          KIFC3_HUMAN   445 NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVGKSGAEGSRLREAQHINKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 766
               SCOP domains d2h58a_ A: automated matches                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2h58A00 A:445-766 Kinesin                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhh.hhhhh..eee......eeeeee..eeeeee..eee....hhhhhhh.hhhhhhhhhh...eeeeee.....hhhhhhh......hhhhhhhhhhhhhhhh....eeeeeeeeeeeee..eeee............ee.......ee......eee.hhhhhhhhhhhhhhhh.........hhhhheeeeeeeeeeee.....eeeeeeeeee.......------hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) KINESIN_MOTOR_2  PDB: A:445-766 UniProt: 445-768                                                                                                                                                                                                                                                                                   PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO--------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.13  PDB: A:445-504 UniProt: 444-504 [INCOMPLETE]     Exon 1.14  PDB: A:505-539          Exon 1.15  PDB: A:540-583 UniProt: 540-583  -----------------------------------------Exon 1.17  PDB: A:625-668 UniProt: 625-668  ----------------------------------------------------------------------------Exon 1.19 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------Exon 1.16  PDB: A:583-624 UniProt: 583-624-------------------------------------------Exon 1.18  PDB: A:668-744 (gaps) UniProt: 668-744                            ---------------------- Transcript 1 (2)
                 2h58 A 445 NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERV------GSRLREAQHINKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 766
                                   454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674      |  -   |   694       704       714       724       734       744       754       764  
                                                                                                                                                                                                                                                                      681    688                                                                              

   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H58)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KIFC3_HUMAN | Q9BVG8)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008569    ATP-dependent microtubule motor activity, minus-end-directed    Catalysis of movement along a microtubule toward the minus end, coupled to the hydrolysis of ATP.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    GO:0003777    microtubule motor activity    Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0007030    Golgi organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.
    GO:0090136    epithelial cell-cell adhesion    The attachment of an epithelial cell to another epithelial cell via adhesion molecules.
    GO:0007018    microtubule-based movement    A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
    GO:0007017    microtubule-based process    Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.
    GO:0007601    visual perception    The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
    GO:0045218    zonula adherens maintenance    Maintaining the zonula adherens junction, the cell-cell adherens junction formed near the apex of epithelial cells.
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:0005912    adherens junction    A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0005871    kinesin complex    Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0005915    zonula adherens    A cell-cell adherens junction which forms a continuous belt near the apex of epithelial cells.

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