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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MONO-ZINC-BOUNDFORM OF NEW DELHI METALLO-BETA-LACTAMASE-1 FROM KLEBSIELLA PNEUMONIAE
 
Authors :  Y. Kim, C. Tesar, R. Jedrzejczak, J. Babnigg, T. A. Binkowski, A. Joachi Midwest Center For Structural Genomics (Mcsg), Structures Of Proteins Conferring Susceptibility To Known Mtb Inhibitors
Date :  13 Jun 11  (Deposition) - 29 Jun 11  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A (1x),D (1x)
Biol. Unit 6:  B (1x),C (1x)
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Alpha-Beta-Beta-Alpha Sandwich, Hydrolase, Periplasmic, Structures Of Mtb Proteins Conferring Susceptibility To Known Mtb Inhibitors, Mtbi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kim, C. Tesar, J. Mire, R. Jedrzejczak, A. Binkowski, G. Babnigg, J. Sacchettini, A. Joachimiak
Structure Of Apo- And Monometalated Forms Of Ndm-1 A Highly Potent Carbapenem-Hydrolyzing Metallo-Beta-Lactamase
Plos One V. 6 24621 2011
PubMed-ID: 21931780  |  Reference-DOI: 10.1371/JOURNAL.PONE.0024621

(-) Compounds

Molecule 1 - BETA-LACTAMASE NDM-1
    ChainsA, B, C, D
    EC Number3.5.2.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7
    Expression System StrainBL21 MAGIC
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentSEQUENCE DATABASE RESIDUES 39-270
    GeneBLANDM-1
    Organism ScientificKLEBSIELLA PNEUMONIAE
    Organism Taxid573
    SynonymNDM-1, METALLO-BETA-LACTAMASE NDM-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D
Biological Unit 5 (1x)A (1x)  D (1x)
Biological Unit 6 (1x) B (1x)C (1x) 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric Unit (5, 19)
No.NameCountTypeFull Name
1CIT4Ligand/IonCITRIC ACID
2CL1Ligand/IonCHLORIDE ION
3GOL5Ligand/IonGLYCEROL
4SO45Ligand/IonSULFATE ION
5ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4SO41Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4SO4-1Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION
Biological Unit 5 (3, 4)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION
Biological Unit 6 (3, 4)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4SO41Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:120 , HIS A:122 , HIS A:189BINDING SITE FOR RESIDUE ZN A 280
02AC2SOFTWAREASP A:43 , VAL A:50 , ARG A:52 , GLN A:60 , THR A:62 , ASN A:76 , SER A:251 , ALA A:252 , ARG D:52 , CIT D:281BINDING SITE FOR RESIDUE CIT A 281
03AC3SOFTWAREARG A:234 , ARG A:264 , ALA B:257BINDING SITE FOR RESIDUE SO4 A 282
04AC4SOFTWARETHR A:260 , HIS A:261 , ARG A:264 , HOH A:291 , ARG B:264BINDING SITE FOR RESIDUE SO4 A 283
05AC5SOFTWAREHOH A:21 , ARG A:256 , ARG B:256BINDING SITE FOR RESIDUE GOL A 284
06AC6SOFTWAREHIS B:120 , HIS B:122 , HIS B:189 , CYS B:208BINDING SITE FOR RESIDUE ZN B 280
07AC7SOFTWAREASP B:43 , VAL B:50 , ARG B:52 , GLN B:60 , THR B:62 , ASN B:76 , SER B:251 , ALA B:252BINDING SITE FOR RESIDUE CIT B 281
08AC8SOFTWAREALA A:257 , ARG B:234 , ARG B:264BINDING SITE FOR RESIDUE SO4 B 282
09AC9SOFTWAREARG A:264 , HOH A:318 , THR B:260 , HIS B:261 , ARG B:264 , HOH B:318 , HOH B:337BINDING SITE FOR RESIDUE SO4 B 283
10BC1SOFTWAREHIS B:159 , SER B:160 , ALA C:165BINDING SITE FOR RESIDUE GOL B 284
11BC2SOFTWAREHIS C:120 , HIS C:122 , HIS C:189 , HOH C:320BINDING SITE FOR RESIDUE ZN C 280
12BC3SOFTWAREASP C:43 , VAL C:50 , ARG C:52 , GLN C:60 , THR C:62 , ALA C:74 , ASN C:76 , SER C:251 , ALA C:252BINDING SITE FOR RESIDUE CIT C 281
13BC4SOFTWAREHIS C:261 , ARG C:264 , ARG D:264BINDING SITE FOR RESIDUE SO4 C 282
14BC5SOFTWAREARG C:256 , ALA C:257 , THR C:260 , HOH C:325 , ARG D:234BINDING SITE FOR RESIDUE GOL C 283
15BC6SOFTWARELYS C:181 , ILE C:198 , ASP C:199 , THR C:201 , ILE C:203BINDING SITE FOR RESIDUE GOL C 284
16BC7SOFTWARELYS C:216BINDING SITE FOR RESIDUE CL C 285
17BC8SOFTWAREHIS D:120 , HIS D:122 , HIS D:189BINDING SITE FOR RESIDUE ZN D 280
18BC9SOFTWAREALA A:252 , CIT A:281 , ASP D:43 , VAL D:50 , ARG D:52 , GLN D:60 , THR D:62 , ASN D:76 , HIS D:250 , SER D:251 , ALA D:252 , HOH D:338BINDING SITE FOR RESIDUE CIT D 281
19CC1SOFTWAREARG C:264 , THR D:260 , HIS D:261 , ARG D:264 , HOH D:314BINDING SITE FOR RESIDUE GOL D 282

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SFP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SFP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SFP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SFP)

(-) Exons   (0, 0)

(no "Exon" information available for 3SFP)

(-) 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:231
 aligned with BLAN1_KLEPN | C7C422 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:231
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269 
          BLAN1_KLEPN    40 ETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
               SCOP domains d3sfpa_ A: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eee.hhhh.................hhhhhhhhhhhhh....eee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sfp A  40 ETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269 

Chain B from PDB  Type:PROTEIN  Length:231
 aligned with BLAN1_KLEPN | C7C422 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:231
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269 
          BLAN1_KLEPN    40 ETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
               SCOP domains d3sfpb_ B: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eeeee....................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sfp B  40 ETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269 

Chain C from PDB  Type:PROTEIN  Length:231
 aligned with BLAN1_KLEPN | C7C422 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:231
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269 
          BLAN1_KLEPN    40 ETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
               SCOP domains d3sfpc_ C: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeeeee..eeeeeeeee.....eeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eee......................hhhhhhhhhhhhh....eee........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sfp C  40 ETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269 

Chain D from PDB  Type:PROTEIN  Length:232
 aligned with BLAN1_KLEPN | C7C422 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:232
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268  
          BLAN1_KLEPN    39 METGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
               SCOP domains d3sfpd_ D: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------Lactamase_B-3sfpD01 D:70-250                                                                                                                                                         -------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------Lactamase_B-3sfpD02 D:70-250                                                                                                                                                         -------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------Lactamase_B-3sfpD03 D:70-250                                                                                                                                                         -------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------Lactamase_B-3sfpD04 D:70-250                                                                                                                                                         -------------------- Pfam domains (4)
         Sec.struct. author .....eee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhh..eeeeehhhhhhhhhh......eee........hhhhh.....eeee...........eeee....eee.hhhh.................hhhhhhhhhhhhh....eee........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sfp D  39 METGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268  

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SFP)

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (BLAN1_KLEPN | C7C422)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0017001    antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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

UniProtKB/Swiss-Prot
        BLAN1_KLEPN | C7C4223pg4 3q6x 3rkj 3rkk 3sbl 3spu 3srx 3zr9 4exs 4exy 4ey2 4eyb 4eyf 4eyl 4gyq 4gyu 4h0d 4hky 4hl1 4hl2 4ram 4raw 4rbs 4rl0 4rl2 4rm5 4u4l 5a5z 5jqj 5k4k 5k4m 5k4n 5n0h 5n0i

(-) Related Entries Specified in the PDB File

3rkj THE SAME PROTEIN, APO-FORM, DIFFERENT CONSTRUCT
3rkk THE SAME PROTEIN, DIFFERENT CRYSTAL FORM
3sbl THE SAME PROTEIN, DIFFERENT CRYSTAL FORM RELATED ID: APC105101 RELATED DB: TARGETDB