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(-) Description

Title :  THE MODULAR ARCHITECTURE OF PROTEIN-PROTEIN BINDING SITE
 
Authors :  D. Reichmann, O. Rahat, S. Albeck, R. Meged, O. Dym, G. Schreiber, Israel Structural Proteomics Center (Ispc)
Date :  07 Nov 04  (Deposition) - 18 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Protein-Protein Complex; Tem-1 Beta-Lactamase; Beta-2 Lactamase Inhibitor Protein; Blip, Israel Structural Proteomics Center, Ispc, Structural Genomics, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Reichmann, O. Rahat, S. Albeck, R. Meged, O. Dym, G. Schreiber
The Modular Architecture Of Protein-Protein Binding Interfaces
Proc. Natl. Acad. Sci. Usa V. 102 57 2005
PubMed-ID: 15618400  |  Reference-DOI: 10.1073/PNAS.0407280102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE TEM
    ChainsA, B
    EC Number3.5.2.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneBLA
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymTEM-1
 
Molecule 2 - BETA-LACTAMASE INHIBITORY PROTEIN
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificSTREPTOMYCES CLAVULIGERUS
    Organism Taxid1901
    SynonymBLIP

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP D:1133 , ARG D:1144BINDING SITE FOR RESIDUE CA D 2001
2AC2SOFTWAREASP C:1133 , ARG C:1144 , ASP C:1163BINDING SITE FOR RESIDUE CA C 2002

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:77 -A:123
2B:77 -B:123
3C:1030 -C:1042
4C:1109 -C:1131
5D:1030 -D:1042
6D:1109 -D:1131

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:166 -Pro A:167
2Tyr C:1119 -Pro C:1120
3Glu B:166 -Pro B:167
4Tyr D:1119 -Pro D:1120

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (10, 20)

Asymmetric Unit (10, 20)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_BLAT_ECOLX_002 *Q37KBLAT_ECOLX  ---  ---A/BQ39K
02UniProtVAR_BLAT_ECOLX_003 *M67LBLAT_ECOLX  ---  ---A/BM69L
03UniProtVAR_BLAT_ECOLX_004 *E102KBLAT_ECOLX  ---  ---A/BA104K
04UniProtVAR_BLAT_ECOLX_005 *R162HBLAT_ECOLX  ---  ---A/BR164H
05UniProtVAR_BLAT_ECOLX_006 *R162SBLAT_ECOLX  ---  ---A/BR164S
06UniProtVAR_BLAT_ECOLX_007 *A235TBLAT_ECOLX  ---  ---A/BA237T
07UniProtVAR_BLAT_ECOLX_008 *G236SBLAT_ECOLX  ---  ---A/BG238S
08UniProtVAR_BLAT_ECOLX_009 *E237KBLAT_ECOLX  ---  ---A/BE239K
09UniProtVAR_BLAT_ECOLX_010 *T261MBLAT_ECOLX  ---  ---A/BT263M
10UniProtVAR_BLAT_ECOLX_011 *N272DBLAT_ECOLX  ---  ---A/BN274D
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (10, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_BLAT_ECOLX_002 *Q37KBLAT_ECOLX  ---  ---AQ39K
02UniProtVAR_BLAT_ECOLX_003 *M67LBLAT_ECOLX  ---  ---AM69L
03UniProtVAR_BLAT_ECOLX_004 *E102KBLAT_ECOLX  ---  ---AA104K
04UniProtVAR_BLAT_ECOLX_005 *R162HBLAT_ECOLX  ---  ---AR164H
05UniProtVAR_BLAT_ECOLX_006 *R162SBLAT_ECOLX  ---  ---AR164S
06UniProtVAR_BLAT_ECOLX_007 *A235TBLAT_ECOLX  ---  ---AA237T
07UniProtVAR_BLAT_ECOLX_008 *G236SBLAT_ECOLX  ---  ---AG238S
08UniProtVAR_BLAT_ECOLX_009 *E237KBLAT_ECOLX  ---  ---AE239K
09UniProtVAR_BLAT_ECOLX_010 *T261MBLAT_ECOLX  ---  ---AT263M
10UniProtVAR_BLAT_ECOLX_011 *N272DBLAT_ECOLX  ---  ---AN274D
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (10, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_BLAT_ECOLX_002 *Q37KBLAT_ECOLX  ---  ---BQ39K
02UniProtVAR_BLAT_ECOLX_003 *M67LBLAT_ECOLX  ---  ---BM69L
03UniProtVAR_BLAT_ECOLX_004 *E102KBLAT_ECOLX  ---  ---BA104K
04UniProtVAR_BLAT_ECOLX_005 *R162HBLAT_ECOLX  ---  ---BR164H
05UniProtVAR_BLAT_ECOLX_006 *R162SBLAT_ECOLX  ---  ---BR164S
06UniProtVAR_BLAT_ECOLX_007 *A235TBLAT_ECOLX  ---  ---BA237T
07UniProtVAR_BLAT_ECOLX_008 *G236SBLAT_ECOLX  ---  ---BG238S
08UniProtVAR_BLAT_ECOLX_009 *E237KBLAT_ECOLX  ---  ---BE239K
09UniProtVAR_BLAT_ECOLX_010 *T261MBLAT_ECOLX  ---  ---BT263M
10UniProtVAR_BLAT_ECOLX_011 *N272DBLAT_ECOLX  ---  ---BN274D
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLAT_ECOLX64-79
 
  2A:66-81
B:66-81
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLAT_ECOLX64-79
 
  1A:66-81
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLAT_ECOLX64-79
 
  1-
B:66-81

(-) Exons   (0, 0)

(no "Exon" information available for 1XXM)

(-) Sequences/Alignments

Asymmetric 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:263
 aligned with BLAT_ECOLX | P62593 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:263
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
          BLAT_ECOLX     24 HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW  286
               SCOP domains d1xxma_ A: beta-Lactamase, class A                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1xxmA00 A:26-288 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..eeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh...hhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh............hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeee.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) -------------K-----------------------------L----------------------------------K-----------------------------------------------------------H------------------------------------------------------------------------TSK-----------------------M----------D-------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------BETA_LACTAMASE_A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xxm A   26 HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVAASPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW  288
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285   

Chain B from PDB  Type:PROTEIN  Length:263
 aligned with BLAT_ECOLX | P62593 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:263
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
          BLAT_ECOLX     24 HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW  286
               SCOP domains d1xxmb_ B: beta-Lactamase, class A                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1xxmB00 B:26-288 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                CATH domains
           Pfam domains (1) -------------------------Beta-lactamase2-1xxmB01 B:51-261                                                                                                                                                                                   --------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------Beta-lactamase2-1xxmB02 B:51-261                                                                                                                                                                                   --------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh...hhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) -------------K-----------------------------L----------------------------------K-----------------------------------------------------------H------------------------------------------------------------------------TSK-----------------------M----------D-------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------BETA_LACTAMASE_A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xxm B   26 HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVAASPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW  288
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285   

Chain C from PDB  Type:PROTEIN  Length:165
 aligned with BLIP_STRCL | P35804 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:165
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196     
          BLIP_STRCL     37 AGVMTGAKFTQIQFGMTRQQVLDIAGAENCETGGSFGDSIHCRGHAAGDYYAYATFGFTSAAADAKVDSKSQEKLLAPSAPTLTLAKFNQVTVGMTRAQVLATVGQGSCTTWSEYYPAYPSTAGVTLSLSCFDVDGYSSTGFYRGSAHLWFTDGVLQGKRQWDLV  201
               SCOP domains d1xxmc_ C: automated matches                                                                                                                                          SCOP domains
               CATH domains 1xxmC01 C:1001-1074  [code=3.30.1450.10, no name defined]                 1xxmC02 C:1075-1165  [code=3.30.1450.10, no name defined]                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh....hhhhhhhhhh...ee.hhhhh..eeeeeeee..eeeeeeeee........eeeeeee..........hhhhhhhh....hhhhhhhhhh...eeeeeee..........eeeeeee.............eeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xxm C 1001 AGVMTGAKFTQIQFGMTRQQVLDIAGAENCETGGSFGDSIHCRGHAAGDYYAYATFGFTSAAADAKVDSKSQEALLAPSAPTLTLAKFNQVTVGMTRAQVLATVGQGSCTTWSEYYPAYPSTAGVTLSLSCFDVDGYSSTGAARGSAHLWFTDGVLQGKRQWDLV 1165
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160     

Chain D from PDB  Type:PROTEIN  Length:165
 aligned with BLIP_STRCL | P35804 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:165
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196     
          BLIP_STRCL     37 AGVMTGAKFTQIQFGMTRQQVLDIAGAENCETGGSFGDSIHCRGHAAGDYYAYATFGFTSAAADAKVDSKSQEKLLAPSAPTLTLAKFNQVTVGMTRAQVLATVGQGSCTTWSEYYPAYPSTAGVTLSLSCFDVDGYSSTGFYRGSAHLWFTDGVLQGKRQWDLV  201
               SCOP domains d1xxmd_ D: automated matches                                                                                                                                          SCOP domains
               CATH domains 1xxmD01 D:1001-1074  [code=3.30.1450.10, no name defined]                 1xxmD02 D:1075-1165  [code=3.30.1450.10, no name defined]                                   CATH domains
           Pfam domains (1) BLIP-1xxmD01 D:1001-1164                                                                                                                                            - Pfam domains (1)
           Pfam domains (2) BLIP-1xxmD02 D:1001-1164                                                                                                                                            - Pfam domains (2)
         Sec.struct. author ....hhhhhhhh....hhhhhhhhhh...eee.hhhh..eeeeeeee..eeeeeeeee........eeeeeee..........hhhhhhhh....hhhhhhhhhh...eeeeeee..........eeeeeee.............eeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xxm D 1001 AGVMTGAKFTQIQFGMTRQQVLDIAGAENCETGGSFGDSIHCRGHAAGDYYAYATFGFTSAAADAKVDSKSQEALLAPSAPTLTLAKFNQVTVGMTRAQVLATVGQGSCTTWSEYYPAYPSTAGVTLSLSCFDVDGYSSTGAARGSAHLWFTDGVLQGKRQWDLV 1165
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160     

   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, 4)

Asymmetric Unit

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: PepSY (8)
(-)
Family: BLIP (4)
2aBLIP-1xxmD01D:1001-1164
2bBLIP-1xxmD02D:1001-1164

(-) Gene Ontology  (6, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BLAT_ECOLX | P62593)
molecular function
    GO:0008800    beta-lactamase activity    Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
    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: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:0030655    beta-lactam antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.
    GO:0046677    response to antibiotic    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 antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

Chain C,D   (BLIP_STRCL | P35804)
molecular function
    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).
cellular component
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BLAT_ECOLX | P625931axb 1bt5 1btl 1ck3 1erm 1ero 1erq 1esu 1fqg 1jtd 1jtg 1jvj 1jwp 1jwv 1jwz 1lhy 1li0 1li9 1m40 1nxy 1ny0 1nym 1nyy 1pzo 1pzp 1s0w 1tem 1xpb 1yt4 1zg4 1zg6 2b5r 2v1z 2v20 3c7u 3c7v 3cmz 3dtm 3jyi 3toi 4dxb 4dxc 4gku 4ibr 4ibx 4id4 4mez 4qy5 4qy6 4r4r 4r4s 4rva 4rx2 4rx3 4zj1 4zj2 4zj3 5hvi 5hw1 5hw5 5i52 5i63 5iq8 5kkf
        BLIP_STRCL | P358041jtg 1s0w 2b5r 2g2u 2g2w 3c4o 3c4p 3c7u 3c7v 3e2k 3e2l 3gmu 3n4i

(-) Related Entries Specified in the PDB File

1s0w 1B LACTAMSE/B LACTAMASE INHIBITOR RELATED ID: W00178 RELATED DB: TARGETDB