Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
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 :  NIKR-OPERATOR DNA COMPLEX
 
Authors :  E. R. Schreiter, C. L. Drennan
Date :  09 Aug 06  (Deposition) - 22 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D,I,J  (1x)
Biol. Unit 2:  E,F,G,H,K,L  (1x)
Keywords :  Nickel, Transcription Factor, Protein-Dna Complex, Ribbon- Helix-Helix, Metal Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. R. Schreiter, S. C. Wang, D. B. Zamble, C. L. Drennan
Nikr-Operator Complex Structure And The Mechanism Of Repressor Activation By Metal Ions.
Proc. Natl. Acad. Sci. Usa V. 103 13676 2006
PubMed-ID: 16945905  |  Reference-DOI: 10.1073/PNAS.0606247103
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*AP*TP*AP*CP*TP*TP*AP*AP*AP *AP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'
    Chains: I, K
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'- D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*TP*TP*TP*TP*AP*AP*GP*TP*AP *TP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'
    Chains: J, L
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - NICKEL-RESPONSIVE REGULATOR
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NIKR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABCD    IJ  
Biological Unit 2 (1x):     EFGH  KL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 35)

Asymmetric Unit (3, 35)
No.NameCountTypeFull Name
1K11Ligand/IonPOTASSIUM ION
2MSE16Mod. Amino AcidSELENOMETHIONINE
3NI8Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
3NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
3NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS B:87 , HIS B:89 , CYS B:95 , HIS D:76BINDING SITE FOR RESIDUE NI D 301
02AC2SOFTWAREHIS A:87 , VAL A:88 , HIS A:89 , CYS A:95 , VAL C:72 , HIS C:76BINDING SITE FOR RESIDUE NI A 302
03AC3SOFTWAREHIS A:76 , HIS C:87 , VAL C:88 , HIS C:89 , CYS C:95BINDING SITE FOR RESIDUE NI C 303
04AC4SOFTWAREVAL B:72 , HIS B:76 , HIS D:87 , HIS D:89 , CYS D:95BINDING SITE FOR RESIDUE NI D 304
05AC5SOFTWAREHIS F:87 , HIS F:89 , CYS F:95 , VAL H:72 , HIS H:76BINDING SITE FOR RESIDUE NI F 305
06AC6SOFTWAREHIS E:87 , VAL E:88 , HIS E:89 , CYS E:95 , VAL G:72 , HIS G:76BINDING SITE FOR RESIDUE NI E 306
07AC7SOFTWAREVAL E:72 , HIS E:76 , HIS G:87 , HIS G:89 , CYS G:95BINDING SITE FOR RESIDUE NI G 307
08AC8SOFTWAREVAL F:72 , HIS F:76 , HIS H:87 , HIS H:89 , CYS H:95BINDING SITE FOR RESIDUE NI H 308
09AC9SOFTWAREGLU A:30 , ASP A:34 , ILE B:116 , GLN B:118 , VAL B:121BINDING SITE FOR RESIDUE K A 401
10BC1SOFTWAREGLU C:30 , ASP C:34 , ILE D:116 , ALA D:117 , GLN D:118 , VAL D:121BINDING SITE FOR RESIDUE K C 402
11BC2SOFTWAREGLU E:30 , ASP E:34 , ILE F:116 , ALA F:117 , GLN F:118 , VAL F:121BINDING SITE FOR RESIDUE K E 403
12BC3SOFTWAREGLU G:30 , ASP G:34 , ILE H:116 , ALA H:117 , GLN H:118 , VAL H:121BINDING SITE FOR RESIDUE K G 404
13BC4SOFTWAREHIS F:89 , HIS H:79 , SER H:82BINDING SITE FOR RESIDUE K H 405
14BC5SOFTWAREHIS E:79 , SER E:82 , HIS G:89BINDING SITE FOR RESIDUE K E 406
15BC6SOFTWAREHIS E:89 , HIS G:79 , SER G:82BINDING SITE FOR RESIDUE K G 407
16BC7SOFTWAREHIS F:79 , SER F:82 , HIS H:89BINDING SITE FOR RESIDUE K F 408
17BC8SOFTWAREHIS A:79 , SER A:82 , HIS C:89BINDING SITE FOR RESIDUE K A 409
18BC9SOFTWAREHIS B:79 , SER B:82 , HIS D:89BINDING SITE FOR RESIDUE K B 410
19CC1SOFTWAREHIS A:89 , HIS C:79 , SER C:82BINDING SITE FOR RESIDUE K C 411

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HZV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HZV)

(-) Exons   (0, 0)

(no "Exon" information available for 2HZV)

(-) 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:131
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           NIKR_ECOLI     1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
               SCOP domains d2hzva1 A:1-48                                  d2hzva2 A:49-131 Nickel responsive regulator NikR, C-terminal domain                SCOP domains
               CATH domains -2hzvA01 A:2-47 Met repressor-like             2hzvA02 A:48-131 ACT-like. Chain A, domain 2                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......eeeeeeeeeee.....hhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeeeehhhhhhhhhhhhhh...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hzv A   1 mQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDmGDVQHFADDVIAQRGVRHGHLQCLPK 131
                            |       10        20        30        40        50        60        70        80        90       100    |  110       120       130 
                            |                                                                                                     105-MSE                      
                            1-MSE                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:131
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           NIKR_ECOLI     1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
               SCOP domains d2hzvb1 B:1-48                                  d2hzvb2 B:49-131 Nickel responsive regulator NikR, C-terminal domain                SCOP domains
               CATH domains -2hzvB01 B:2-47 Met repressor-like             2hzvB02 B:48-131 ACT-like. Chain A, domain 2                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh........eeeeeeeeeee.hhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhh...eeeee..eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hzv B   1 mQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDmGDVQHFADDVIAQRGVRHGHLQCLPK 131
                            |       10        20        30        40        50        60        70        80        90       100    |  110       120       130 
                            1-MSE                                                                                                 105-MSE                      


Chain C from PDB  Type:PROTEIN  Length:131
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           NIKR_ECOLI     1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
               SCOP domains d2hzvc1 C:1-48                                  d2hzvc2 C:49-131 Nickel responsive regulator NikR, C-terminal domain                SCOP domains
               CATH domains -2hzvC01 C:2-47 Met repressor-like             2hzvC02 C:48-131 ACT-like. Chain A, domain 2                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee..hhhhhhhhhhhhhhh...eeeeeee.....eeeeeeeeeeehhhhhhhhhhhhh....eeee..ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hzv C   1 mQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDmGDVQHFADDVIAQRGVRHGHLQCLPK 131
                            |       10        20        30        40        50        60        70        80        90       100    |  110       120       130 
                            1-MSE                                                                                                 105-MSE                      


Chain D from PDB  Type:PROTEIN  Length:131
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           NIKR_ECOLI     1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
               SCOP domains d2hzvd1 D:1-48                                  d2hzvd2 D:49-131 Nickel responsive regulator NikR, C-terminal domain                SCOP domains
               CATH domains -2hzvD01 D:2-47 Met repressor-like             2hzvD02 D:48-131 ACT-like. Chain A, domain 2                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh........eeeeeeeeeee.hhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhh.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hzv D   1 mQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDmGDVQHFADDVIAQRGVRHGHLQCLPK 131
                            |       10        20        30        40        50        60        70        80        90       100    |  110       120       130 
                            1-MSE                                                                                                 105-MSE                      


Chain E from PDB  Type:PROTEIN  Length:131
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           NIKR_ECOLI     1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
               SCOP domains d2hzve1 E:1-48                                  d2hzve2 E:49-131 Nickel responsive regulator NikR, C-terminal domain                SCOP domains
               CATH domains -2hzvE01 E:2-47 Met repressor-like             2hzvE02 E:48-131 ACT-like. Chain A, domain 2                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee.....hhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeeeehhhhhhhhhhhhhh...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hzv E   1 mQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDmGDVQHFADDVIAQRGVRHGHLQCLPK 131
                            |       10        20        30        40        50        60        70        80        90       100    |  110       120       130 
                            1-MSE                                                                                                 105-MSE                      


Chain F from PDB  Type:PROTEIN  Length:131
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           NIKR_ECOLI     1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
               SCOP domains d2hzvf1 F:1-48                                  d2hzvf2 F:49-131 Nickel responsive regulator NikR, C-terminal domain                SCOP domains
               CATH domains -2hzvF01 F:2-47 Met repressor-like             2hzvF02 F:48-131 ACT-like. Chain A, domain 2                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh........eeeeeeeeeee.hhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhh...eeeee..eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hzv F   1 mQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDmGDVQHFADDVIAQRGVRHGHLQCLPK 131
                            |       10        20        30        40        50        60        70        80        90       100    |  110       120       130 
                            1-MSE                                                                                                 105-MSE                      


Chain G from PDB  Type:PROTEIN  Length:131
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           NIKR_ECOLI     1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
               SCOP domains d2hzvg1 G:1-48                                  d2hzvg2 G:49-131 Nickel responsive regulator NikR, C-terminal domain                SCOP domains
               CATH domains -2hzvG01 G:2-47 Met repressor-like             2hzvG02 G:48-131 ACT-like. Chain A, domain 2                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee....hhhhhhhhhhhhh...eeeeeee.....eeeeeeeeeeehhhhhhhhhhhhh....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hzv G   1 mQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDmGDVQHFADDVIAQRGVRHGHLQCLPK 131
                            |       10        20        30        40        50        60        70        80        90       100    |  110       120       130 
                            1-MSE                                                                                                 105-MSE                      


Chain H from PDB  Type:PROTEIN  Length:131
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           NIKR_ECOLI     1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
               SCOP domains d2hzvh1 H:1-48                                  d2hzvh2 H:49-131 Nickel responsive regulator NikR, C-terminal domain                SCOP domains
               CATH domains -2hzvH01 H:2-47 Met repressor-like             2hzvH02 H:48-131 ACT-like. Chain A, domain 2                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh........eeeeeeeeeee.hhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhh.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hzv H   1 mQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDmGDVQHFADDVIAQRGVRHGHLQCLPK 131
                            |       10        20        30        40        50        60        70        80        90       100    |  110       120       130 
                            1-MSE                                                                                                 105-MSE                      


Chain I from PDB  Type:DNA  Length:30
                                                              
                 2hzv I   1 AGTATGACGAATACTTAAAATCGTCATACT  30
                                    10        20        30


Chain J from PDB  Type:DNA  Length:30
                                                              
                 2hzv J   1 AGTATGACGATTTTAAGTATTCGTCATACT  30
                                    10        20        30


Chain K from PDB  Type:DNA  Length:30
                                                              
                 2hzv K   1 AGTATGACGAATACTTAAAATCGTCATACT  30
                                    10        20        30


Chain L from PDB  Type:DNA  Length:30
                                                              
                 2hzv L   1 AGTATGACGATTTTAAGTATTCGTCATACT  30
                                    10        20        30
   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, 16)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 16)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: 2-Layer Sandwich (8480)
(-)
Topology: Alpha-Beta Plaits (1688)
(-)
Homologous Superfamily: ACT-like. Chain A, domain 2 (9)
(-)
[unclassified] (1)
1a2hzvA02A:48-131
1b2hzvB02B:48-131
1c2hzvC02C:48-131
1d2hzvD02D:48-131
1e2hzvE02E:48-131
1f2hzvF02F:48-131
1g2hzvG02G:48-131
1h2hzvH02H:48-131
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (NIKR_ECOLI | P0A6Z6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016151    nickel cation binding    Interacting selectively and non-covalently with nickel (Ni) cations.
    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:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0010045    response to nickel cation    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 nickel cation stimulus.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

 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
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2hzv)
 
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
  2hzv
    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
  NIKR_ECOLI | P0A6Z6
    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)
  (no 'Enzyme Classificator' available)
    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
  NIKR_ECOLI | P0A6Z6
    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
        NIKR_ECOLI | P0A6Z6: 1q5v 1q5y 2hza 3bkf 3bkt 3bku 3od2

(-) Related Entries Specified in the PDB File

1q5v NI-MBD NIKR
1q5y FULL-LENGTH APO NIKR
2hza FULL-LENGTH NI-NIKR