Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  X-RAY STRUCTURE OF THE REDUCED NIKA/1 HYBRID, NIKA/1-RED
 
Authors :  C. Cavazza, C. Bochot, P. Rousselot-Pailley, P. Carpentier, M. V. Cher L. Martin, C. Marchi-Delapierre, J. C. Fontecilla-Camps, S. Menage
Date :  05 May 10  (Deposition) - 09 Feb 11  (Release) - 09 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein-Bound Iron Complex, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Cavazza, C. Bochot, P. Rousselot-Pailley, P. Carpentier, M. V. Cherrier, L. Martin, C. Marchi-Delapierre, J. C. Fontecilla-Camps, S. Menage
Crystallographic Snapshots Of The Reaction Of Aromatic C-H With O(2) Catalysed By A Protein-Bound Iron Complex
Nat. Chem. V. 2 1069 2010
PubMed-ID: 21107372  |  Reference-DOI: 10.1038/NCHEM.841

(-) Compounds

Molecule 1 - NICKEL-BINDING PERIPLASMIC PROTEIN
    Chains: A, B
    EC Number: 3.6.3.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NIKA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: NIKA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 20)

Asymmetric Unit (8, 20)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2BHZ2Ligand/Ion2-[2-[CARBOXYMETHYL(PHENYLMETHYL)AMINO]ETHYL-[(2-HYDROXYPHENYL)METHYL]AMINO]ETHANOIC ACID
3CL2Ligand/IonCHLORIDE ION
4DTU2Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
5DTV1Ligand/Ion(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
6FE22Ligand/IonFE (II) ION
7GOL5Ligand/IonGLYCEROL
8SO41Ligand/IonSULFATE ION
Biological Unit 1 (6, 13)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2BHZ1Ligand/Ion2-[2-[CARBOXYMETHYL(PHENYLMETHYL)AMINO]ETHYL-[(2-HYDROXYPHENYL)METHYL]AMINO]ETHANOIC ACID
3CL-1Ligand/IonCHLORIDE ION
4DTU2Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
5DTV-1Ligand/Ion(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
6FE21Ligand/IonFE (II) ION
7GOL3Ligand/IonGLYCEROL
8SO41Ligand/IonSULFATE ION
Biological Unit 2 (4, 5)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2BHZ1Ligand/Ion2-[2-[CARBOXYMETHYL(PHENYLMETHYL)AMINO]ETHYL-[(2-HYDROXYPHENYL)METHYL]AMINO]ETHANOIC ACID
3CL-1Ligand/IonCHLORIDE ION
4DTU-1Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
5DTV1Ligand/Ion(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
6FE21Ligand/IonFE (II) ION
7GOL2Ligand/IonGLYCEROL
8SO4-1Ligand/IonSULFATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREBHZ A:504 , HOH A:520BINDING SITE FOR RESIDUE FE2 A 503
02AC2SOFTWARETYR A:22 , MET A:27 , ARG A:97 , TRP A:100 , ARG A:137 , TRP A:398 , HIS A:416 , THR A:490 , FE2 A:503 , HOH A:520 , HOH A:556 , HOH A:572BINDING SITE FOR RESIDUE BHZ A 504
03AC3SOFTWARELYS A:52 , ARG A:68 , ASP A:69 , ASP A:70 , HOH A:529BINDING SITE FOR RESIDUE ACT A 505
04AC4SOFTWAREASN A:261 , LEU A:263 , HOH A:802BINDING SITE FOR RESIDUE ACT A 506
05AC5SOFTWAREASN A:235 , ALA A:237 , GLN A:423 , HOH A:819BINDING SITE FOR RESIDUE ACT A 507
06AC6SOFTWAREASN A:482 , PRO A:484 , GLN A:496 , HOH A:814BINDING SITE FOR RESIDUE ACT A 508
07AC7SOFTWAREARG A:384 , ARG A:389 , LEU B:430 , ARG B:457BINDING SITE FOR RESIDUE SO4 A 509
08AC8SOFTWARELEU A:167 , GLN A:168 , HOH A:627 , THR B:204 , ALA B:208 , THR B:211 , ASP B:213BINDING SITE FOR RESIDUE GOL A 510
09AC9SOFTWARESER A:233 , HOH B:808BINDING SITE FOR RESIDUE CL A 512
10BC1SOFTWARETRP A:10 , GLY A:219 , ASN A:220 , GLY A:222 , LEU A:223 , GOL A:516 , HOH A:826BINDING SITE FOR RESIDUE DTU A 513
11BC2SOFTWAREHIS A:56BINDING SITE FOR RESIDUE DTU A 514
12BC3SOFTWAREASN A:220 , ILE A:246 , GLU A:247 , ARG A:396 , THR A:490 , DTU A:513 , HOH A:553 , HOH A:779 , HOH A:838BINDING SITE FOR RESIDUE GOL A 516
13BC4SOFTWARETHR A:23 , GLN A:26 , HOH A:625 , HOH A:708 , HOH A:894BINDING SITE FOR RESIDUE ACT A 517
14BC5SOFTWAREARG A:89 , LEU A:92 , ARG A:95 , VAL A:108 , ASP A:109 , VAL A:110 , ASN A:281 , HOH A:795 , HOH A:799BINDING SITE FOR RESIDUE GOL A 515
15BC6SOFTWAREBHZ B:504 , HOH B:778BINDING SITE FOR RESIDUE FE2 B 503
16BC7SOFTWARETYR B:22 , MET B:27 , ARG B:97 , TRP B:100 , ARG B:137 , TRP B:398 , THR B:490 , FE2 B:503 , HOH B:551 , HOH B:573 , HOH B:778 , HOH B:780BINDING SITE FOR RESIDUE BHZ B 504
17BC8SOFTWAREMET B:27 , PHE B:28 , HOH B:816BINDING SITE FOR RESIDUE CL B 506
18BC9SOFTWAREPRO B:11 , GLY B:219 , ASN B:220 , LEU B:223 , GOL B:508BINDING SITE FOR RESIDUE DTV B 507
19CC1SOFTWARETHR B:23 , GLN B:26 , HOH B:570 , HOH B:879BINDING SITE FOR RESIDUE GOL B 509
20CC2SOFTWAREASN B:220 , GLU B:247 , ARG B:396 , ALA B:489 , THR B:490 , DTV B:507 , HOH B:563 , HOH B:721BINDING SITE FOR RESIDUE GOL B 508

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Thr A:23 -Pro A:24
2Arg A:137 -Pro A:138
3Ala A:258 -Pro A:259
4Ala A:400 -Pro A:401
5Asp A:403 -Pro A:404
6Thr B:23 -Pro B:24
7Arg B:137 -Pro B:138
8Ala B:258 -Pro B:259
9Ala B:328 -Gly B:329
10Ala B:400 -Pro B:401
11Asp B:403 -Pro B:404

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SBP_BACTERIAL_5PS01040 Bacterial extracellular solute-binding proteins, family 5 signature.NIKA_ECOLI73-95
 		  2A:51-73
B:51-73
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SBP_BACTERIAL_5PS01040 Bacterial extracellular solute-binding proteins, family 5 signature.NIKA_ECOLI73-95
 		  1A:51-73
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SBP_BACTERIAL_5PS01040 Bacterial extracellular solute-binding proteins, family 5 signature.NIKA_ECOLI73-95
 		  1-
B:51-73

(-) Exons   (0, 0)

(no "Exon" information available for 3MVX)

(-) 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:497
 aligned with NIKA_ECOLI | P33590 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:497
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       
           NIKA_ECOLI    25 PDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKP 521
               SCOP domains d3mvxa_ A: Nickel-binding periplasmic protein NikA                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...............hhhhhhhhh...eee.....eee..eeeeee.....eeeeee............hhhhhhhhhhhhhhhhhhhh.hhhhhheeeeee....eeeeee.....hhhhhhh........hhh.ee..eeeeee........eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeee.....hhhhhhhhhh....eeee....eeeeeee........hhhhhhhhhhhhhhhhhhhhhh....ee.....................hhhhhhhhhhhh...........ee..ee.eeeeeee..hhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh...eeeee.......hhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..eeeeeee..eeee.hhhh...........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------SBP_BACTERIAL_5        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mvx A   3 PDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKP 499
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       


Chain B from PDB  Type:PROTEIN  Length:497
 aligned with NIKA_ECOLI | P33590 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:497
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       
           NIKA_ECOLI    25 PDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKP 521
               SCOP domains d3mvxb_ B: Nickel-binding periplasmic protein NikA                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------SBP_bac_5-3mvxB01 B:45-419                                                                                                                                                                                                                                                                                                                                                             -------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------SBP_bac_5-3mvxB02 B:45-419                                                                                                                                                                                                                                                                                                                                                             -------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee...............hhhhhhhhh...eee.....eee..eeeeee.....eeeeee............hhhhhhhhhhhhhhhhhhhh.hhhhhheeeeee....eeeeee.....hhhhhhh........hhh.ee..eeeeee........eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeee.....hhhhhhhhhh....eeeeeeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhhh....ee.....................hhhhhhhhhhhh...........ee..ee.eeeeeee..hhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh...eeeee.......hhhhhhhh....hhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee.hhhh...........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------SBP_BACTERIAL_5        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mvx B   3 PDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKP 499
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NIKA_ECOLI | P33590)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0016151    nickel cation binding    Interacting selectively and non-covalently with nickel (Ni) cations.
    GO:0015197    peptide transporter activity    Enables the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells.
    GO:0046914    transition metal ion binding    Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
    GO:0050919    negative chemotaxis    The directed movement of a motile cell or organism towards a lower concentration of a chemical.
    GO:0015675    nickel cation transport    The directed movement of nickel (Ni) cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0015833    peptide transport    The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0043190    ATP-binding cassette (ABC) transporter complex    A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    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).

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BHZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DTU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DTV  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:258 - Pro A:259   [ RasMol ]  
    Ala A:400 - Pro A:401   [ RasMol ]  
    Ala B:258 - Pro B:259   [ RasMol ]  
    Ala B:328 - Gly B:329   [ RasMol ]  
    Ala B:400 - Pro B:401   [ RasMol ]  
    Arg A:137 - Pro A:138   [ RasMol ]  
    Arg B:137 - Pro B:138   [ RasMol ]  
    Asp A:403 - Pro A:404   [ RasMol ]  
    Asp B:403 - Pro B:404   [ RasMol ]  
    Thr A:23 - Pro A:24   [ RasMol ]  
    Thr B:23 - Pro B:24   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3mvx
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NIKA_ECOLI | P33590
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.6.3.24
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  NIKA_ECOLI | P33590
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NIKA_ECOLI | P33590: 1uiu 1uiv 1zlq 2noo 3dp8 3e3k 3mvw 3mvy 3mvz 3mw0 3mz9 3mzb 3qim 4dcx 4dcy 4i8c 4i9d 5l8d 5mwu

(-) Related Entries Specified in the PDB File

3mvw 3mvy 3mvz 3mw0 3mz9 3mzb