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(-) Description

Title :  BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM AND LYSOPHOSPHOTIDYLSERINE
 
Authors :  M. Huang, G. Huang, B. Furie, B. Seaton, B. C. Furie
Date :  06 Jan 03  (Deposition) - 16 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Huang, A. C. Rigby, X. Morelli, M. A. Grant, G. Huang, B. Furie, B. Seaton, B. C. Furie
Structural Basis Of Membrane Binding By Gla Domains Of Vitamin K-Dependent Proteins.
Nat. Struct. Biol. V. 10 751 2003
PubMed-ID: 12923575  |  Reference-DOI: 10.1038/NSB971

(-) Compounds

Molecule 1 - PROTHROMBIN
    ChainsA
    EC Number3.4.21.5
    FragmentFRAGMENT 1 (RESIDUES 1-156)
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 24)

Asymmetric/Biological Unit (5, 24)
No.NameCountTypeFull Name
1CA7Ligand/IonCALCIUM ION
2CGU10Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID
3CL3Ligand/IonCHLORIDE ION
4LPS1Ligand/IonO-{HYDROXY[((2R)-2-HYDROXY-3-{[(1S)-1-HYDROXYPENTADECYL]OXY}PROPYL)OXY]PHOSPHORYL}-L-SERINE
5NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:77 , GLU A:112 , PHE A:114 , NAG A:302BINDING SITE FOR RESIDUE NAG A 301
02AC2SOFTWARENAG A:301BINDING SITE FOR RESIDUE NAG A 302
03AC3SOFTWAREASN A:101 , SER A:102 , THR A:103BINDING SITE FOR RESIDUE NAG A 303
04AC4SOFTWARECGU A:26 , CGU A:30BINDING SITE FOR RESIDUE CA A 201
05AC5SOFTWARECGU A:8 , CGU A:27 , CGU A:30 , HOH A:504 , HOH A:507 , HOH A:509BINDING SITE FOR RESIDUE CA A 202
06AC6SOFTWARECGU A:8 , CGU A:17 , CGU A:27 , CGU A:30 , CA A:204 , HOH A:514 , HOH A:519 , HOH A:522BINDING SITE FOR RESIDUE CA A 203
07AC7SOFTWAREALA A:1 , ASN A:2 , CGU A:7 , CGU A:8 , CGU A:17 , CGU A:27 , CA A:203BINDING SITE FOR RESIDUE CA A 204
08AC8SOFTWAREALA A:1 , CGU A:7 , CGU A:17 , CGU A:21 , LPS A:451 , HOH A:527BINDING SITE FOR RESIDUE CA A 205
09AC9SOFTWARECGU A:21 , LPS A:451 , HOH A:557BINDING SITE FOR RESIDUE CA A 206
10BC1SOFTWARECGU A:15 , CGU A:20 , HOH A:537BINDING SITE FOR RESIDUE CA A 207
11BC2SOFTWARETRP A:126 , ARG A:136 , HOH A:513 , HOH A:560BINDING SITE FOR RESIDUE CL A 250
12BC3SOFTWARELYS A:97 , ARG A:135 , GLN A:146BINDING SITE FOR RESIDUE CL A 251
13BC4SOFTWAREARG A:91 , GLU A:112BINDING SITE FOR RESIDUE CL A 252
14BC5SOFTWARELYS A:3 , PHE A:5 , LEU A:6 , CGU A:7 , ARG A:10 , ARG A:16 , CGU A:17 , CGU A:21 , SER A:34 , ALA A:37 , CA A:205 , CA A:206 , HOH A:545 , HOH A:550 , HOH A:557BINDING SITE FOR RESIDUE LPS A 451

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:18 -A:23
2A:48 -A:61
3A:66 -A:144
4A:87 -A:127
5A:115 -A:139

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:53 -Pro A:54
2Tyr A:94 -Pro A:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NL2)

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLA_2PS50998 Gla domain profile.THRB_BOVIN44-90  1A:1-47
2GLA_1PS00011 Vitamin K-dependent carboxylation domain.THRB_BOVIN60-85  1A:17-42
3KRINGLE_2PS50070 Kringle domain profile.THRB_BOVIN108-187
213-292
  1A:65-144
-
4KRINGLE_1PS00021 Kringle domain signature.THRB_BOVIN157-170
262-275
  1A:114-127
-

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000094061ENSBTAE00000076598chr15:77004894-77005007114THRB_BOVIN1-27270--
1.2ENSBTAT000000094062ENSBTAE00000076606chr15:77005352-77005515164THRB_BOVIN27-81551A:1-3838
1.3ENSBTAT000000094063ENSBTAE00000306249chr15:77006130-7700615425THRB_BOVIN82-9091A:39-479
1.4ENSBTAT000000094064ENSBTAE00000076608chr15:77006384-7700643451THRB_BOVIN90-107181A:47-6418
1.5ENSBTAT000000094065ENSBTAE00000076609chr15:77007812-77007917106THRB_BOVIN107-142361A:64-9936
1.6ENSBTAT000000094066ENSBTAE00000076610chr15:77008015-77008151137THRB_BOVIN142-188471A:99-14547
1.7ENSBTAT000000094067ENSBTAE00000076611chr15:77009362-77009676315THRB_BOVIN188-2931061A:145-1462
1.8ENSBTAT000000094068ENSBTAE00000076614chr15:77009972-77010106135THRB_BOVIN293-338460--
1.9ENSBTAT000000094069ENSBTAE00000076615chr15:77010182-77010308127THRB_BOVIN338-380430--
1.10ENSBTAT0000000940610ENSBTAE00000076616chr15:77011290-77011457168THRB_BOVIN380-436570--
1.11ENSBTAT0000000940611ENSBTAE00000076617chr15:77011956-77012129174THRB_BOVIN436-494590--
1.12ENSBTAT0000000940612ENSBTAE00000306240chr15:77012378-77012559182THRB_BOVIN494-555620--
1.13ENSBTAT0000000940613ENSBTAE00000076620chr15:77018853-7701892371THRB_BOVIN555-578240--
1.14ENSBTAT0000000940614ENSBTAE00000076621chr15:77019058-77019320263THRB_BOVIN579-625470--

(-) 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:146
 aligned with THRB_BOVIN | P00735 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:146
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183      
           THRB_BOVIN    44 ANKGFLEEVRKGNLERECLEEPCSREEAFEALESLSATDAFWAKYTACESARNPREKLNECLEGNCAEGVGMNYRGNVSVTRSGIECQLWRSRYPHKPEINSTTHPGADLRENFCRNPDGSITGPWCYTTSPTLRREECSVPVCGQ 189
               SCOP domains d1nl2a2 A:1-65 Prothrombin                                       d1nl2a1 A:66-146 Prothrombin                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Gla-1nl2A01 A:6-47                        ------------------Kringle-1nl2A02 A:66-144                                                       -- Pfam domains
         Sec.struct. author .....hhhhh..hhhhhh.....hhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.............................................................eee.......eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) GLA_2  PDB: A:1-47 UniProt: 44-90              -----------------KRINGLE_2  PDB: A:65-144 UniProt: 108-187                                       -- PROSITE (1)
                PROSITE (2) ----------------GLA_1  PDB: A:17-42       -----------------------------------------------------------------------KRINGLE_1     ------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:1-38 UniProt: 27-81  Exon 1.3 ----------------Exon 1.5  PDB: A:64-99              ---------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.4          ----------------------------------Exon 1.6  PDB: A:99-145 UniProt: 142-188       - Transcript 1 (2)
                 1nl2 A   1 ANKGFLeeVRKGNLeReCLeePCSReeAFeALeSLSATDAFWAKYTACESARNPREKLNECLEGNCAEGVGMNYRGNVSVTRSGIECQLWRSRYPHKPEINSTTHPGADLRENFCRNPDGSITGPWCYTTSPTLRREECSVPVCGQ 146
                                  ||10    | | 20|    || 30  |     40        50        60        70        80        90       100       110       120       130       140      
                                  7-CGU  15-CGU||    ||  |  |                                                                                                                 
                                   8-CGU   17-CGU    ||  |  |                                                                                                                 
                                              20-CGU ||  |  |                                                                                                                 
                                               21-CGU||  |  |                                                                                                                 
                                                    26-CGU  |                                                                                                                 
                                                     27-CGU |                                                                                                                 
                                                        30-CGU                                                                                                                
                                                           33-CGU                                                                                                             

   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  (0, 0)

(no "CATH Domain" information available for 1NL2)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (THRB_BOVIN | P00735)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0070051    fibrinogen binding    Interacting selectively and non-covalently with fibrinogen, a highly soluble hexameric glycoprotein complex that is found in blood plasma and is converted to fibrin by thrombin in the coagulation cascade.
    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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    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).
    GO:0070053    thrombospondin receptor activity    Combining with thrombospondin and transmitting the signal to initiate a change in cell activity.
biological process
    GO:0006953    acute-phase response    An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
    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:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    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:0048712    negative regulation of astrocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of astrocyte differentiation.
    GO:0045861    negative regulation of proteolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0030194    positive regulation of blood coagulation    Any process that activates or increases the frequency, rate or extent of blood coagulation.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0032967    positive regulation of collagen biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
    GO:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:1900738    positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of phospholipase C-activating G-protein coupled receptor signaling pathway.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    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:0051281    positive regulation of release of sequestered calcium ion into cytosol    Any process that activates or increases the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.
    GO:0051258    protein polymerization    The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0051480    regulation of cytosolic calcium ion concentration    Any process involved in the maintenance of an internal steady state of calcium ions within the cytosol of a cell or between the cytosol and its surroundings.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0009611    response to wounding    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 damage to the organism.
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        THRB_BOVIN | P007351a0h 1avg 1bbr 1etr 1ets 1ett 1hrt 1id5 1mkw 1mkx 1nl1 1tbq 1tbr 1toc 1ucy 1uvt 1uvu 1vit 1ycp 2a1d 2hpp 2ody 2pf1 2pf2 2spt 3pma 3pmb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1NL2)