Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - 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 :  NMB1532 PROTEIN FROM NEISSERIA MENINGITIDIS, UNKNOWN FUNCTION
 
Authors :  J. Osipiuk, H. Li, M. Bargassa, A. Joachimiak, Midwest Center For St Genomics (Mcsg)
Date :  28 Feb 07  (Deposition) - 27 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.41
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Apc83866, Unknown Function, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, H. Li, M. Bargassa, A. Joachimiak
X-Ray Crystal Structure Of Nmb1532 Protein Of Unknown Function From Neisseria Meningitidis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN NMB1532
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NMB1532
    Organism Scientific: NEISSERIA MENINGITIDIS
    Organism Taxid: 122586
    Strain: MC58

 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  (5, 17)

Asymmetric Unit (5, 17)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2CL2Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4MN4Ligand/IonMANGANESE (II) ION
5MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CL-1Ligand/IonCHLORIDE ION
3GOL-1Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:22 , HIS A:66 , GLU A:70 , GLU A:140 , MN A:605 , CL A:608BINDING SITE FOR RESIDUE MN A 604
2AC2SOFTWAREGLU A:70 , HIS A:96 , HIS A:136 , GLU A:140 , MN A:604 , CL A:608BINDING SITE FOR RESIDUE MN A 605
3AC3SOFTWAREGLU B:70 , HIS B:96 , HIS B:136 , GLU B:140 , MN B:607 , CL B:609BINDING SITE FOR RESIDUE MN B 606
4AC4SOFTWAREHIS B:22 , HIS B:66 , GLU B:70 , GLU B:140 , MN B:606 , CL B:609BINDING SITE FOR RESIDUE MN B 607
5AC5SOFTWAREHIS A:66 , HIS A:67 , GLU A:70 , HIS A:136 , GLU A:140 , MN A:604 , MN A:605BINDING SITE FOR RESIDUE CL A 608
6AC6SOFTWAREHIS B:66 , HIS B:67 , GLU B:70 , HIS B:136 , GLU B:140 , MN B:606 , MN B:607BINDING SITE FOR RESIDUE CL B 609
7AC7SOFTWARECYS A:21 , TYR A:58 , ALA A:62 , ARG A:167 , HOH A:664BINDING SITE FOR RESIDUE BME A 601
8AC8SOFTWARECYS B:21 , LYS B:24 , TYR B:58 , HOH B:787BINDING SITE FOR RESIDUE BME B 602
9AC9SOFTWAREILE A:139 , HOH A:628 , ALA B:131 , ASP B:134 , THR B:149 , HOH B:664 , HOH B:695BINDING SITE FOR RESIDUE GOL B 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P0N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P0N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P0N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P0N)

(-) Exons   (0, 0)

(no "Exon" information available for 2P0N)

(-) 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:161
 aligned with Q9JYL1_NEIMB | Q9JYL1 from UniProtKB/TrEMBL  Length:169

    Alignment length:161
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168 
         Q9JYL1_NEIMB     9 VTFAEPIEMLYACHGKVRRFCGQVAMLSDYIAENGCNQIVLQTIRQIAQYFNVAAPLHHEDEEENFFPLLLQYAPQAQESVDELLRQHIGLHDNWAAVSAEFAKLEADNAYVPDEEAFKRFVAGYDVHLAIEEPLFDMGNTFIPKEKLTEIGEIMAARRRK 169
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2p0nA00 A:9-169 nmb1532 protein domain like                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p0n A   9 VTFAEPIEmLYACHGKVRRFCGQVAmLSDYIAENGCNQIVLQTIRQIAQYFNVAAPLHHEDEEENFFPLLLQYAPQAQESVDELLRQHIGLHDNWAAVSAEFAKLEADNAYVPDEEAFKRFVAGYDVHLAIEEPLFDmGNTFIPKEKLTEIGEImAARRRK 169
                                    18        28     |  38        48        58        68        78        88        98       108       118       128       138       148       158    |  168 
                                   17-MSE           34-MSE                                                                                                         146-MSE          163-MSE  


Chain B from PDB  Type:PROTEIN  Length:158
 aligned with Q9JYL1_NEIMB | Q9JYL1 from UniProtKB/TrEMBL  Length:169

    Alignment length:158
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
         Q9JYL1_NEIMB    12 AEPIEMLYACHGKVRRFCGQVAMLSDYIAENGCNQIVLQTIRQIAQYFNVAAPLHHEDEEENFFPLLLQYAPQAQESVDELLRQHIGLHDNWAAVSAEFAKLEADNAYVPDEEAFKRFVAGYDVHLAIEEPLFDMGNTFIPKEKLTEIGEIMAARRRK 169
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2p0nB00 B:12-169 nmb1532 protein domain like                                                                                                                   CATH domains
           Pfam domains (1) -Hemerythrin-2p0nB01 B:13-146                                                                                                          ----------------------- Pfam domains (1)
           Pfam domains (2) -Hemerythrin-2p0nB02 B:13-146                                                                                                          ----------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p0n B  12 AEPIEmLYACHGKVRRFCGQVAmLSDYIAENGCNQIVLQTIRQIAQYFNVAAPLHHEDEEENFFPLLLQYAPQAQESVDELLRQHIGLHDNWAAVSAEFAKLEADNAYVPDEEAFKRFVAGYDVHLAIEEPLFDmGNTFIPKEKLTEIGEImAARRRK 169
                                 |  21        31  |     41        51        61        71        81        91       101       111       121       131       141    |  151       161 |      
                                17-MSE           34-MSE                                                                                                         146-MSE          163-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 2P0N)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Hemerythrin] (2)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9JYL1_NEIMB | Q9JYL1)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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
    BME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2p0n)
 
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
  2p0n
    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
  Q9JYL1_NEIMB | Q9JYL1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q9JYL1_NEIMB | Q9JYL1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2P0N)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2P0N)