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(-) Description

Title :  CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE B FROM TRYPANOSOMA BRUCEI, UDP-BOUND FORM
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  10 May 12  (Deposition) - 30 May 12  (Release) - 30 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Ssgcid, Nih, Niaid, Sbri, Emerald Biostructures, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid), A. S. Gardberg, T. E. Edwards, B. Staker, L. Stewart
Crystal Structure Of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei, Udp-Bound Form
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE
    Chains: A, B, C
    EC Number: 2.7.4.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TB11.01.7800
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid: 999953
    Strain: 927/4 GUTAT10.1
    Synonym: NUCLEOSIDE DIPHOSPHATE KINASE B

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2UDP3Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2UDP6Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:11 , TYR A:51 , LEU A:54 , PHE A:59 , LEU A:63 , ARG A:87 , THR A:93 , VAL A:111 , ASN A:114 , MG A:202 , HOH A:311 , HOH A:316 , HOH A:330 , HOH A:384 , HOH A:385 , HOH A:407BINDING SITE FOR RESIDUE UDP A 201
2AC2SOFTWAREUDP A:201 , HOH A:384 , HOH A:385BINDING SITE FOR RESIDUE MG A 202
3AC3SOFTWARELYS B:11 , LEU B:54 , PHE B:59 , LEU B:63 , ARG B:87 , THR B:93 , VAL B:111 , GLY B:112 , ASN B:114 , MG B:202 , HOH B:302 , HOH B:356 , HOH B:365 , HOH B:395 , HOH B:406 , HOH C:420BINDING SITE FOR RESIDUE UDP B 201
4AC4SOFTWAREUDP B:201 , HOH B:356 , HOH B:406BINDING SITE FOR RESIDUE MG B 202
5AC5SOFTWARELYS C:11 , TYR C:51 , LEU C:54 , PHE C:59 , LEU C:63 , ARG C:87 , THR C:93 , VAL C:111 , ASN C:114 , MG C:202 , HOH C:312 , HOH C:321 , HOH C:381 , HOH C:382 , HOH C:383 , HOH C:386 , HOH C:387 , HOH C:408 , HOH C:435BINDING SITE FOR RESIDUE UDP C 201
6AC6SOFTWAREUDP C:201 , HOH C:381 , HOH C:382 , HOH C:383BINDING SITE FOR RESIDUE MG C 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F4A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F4A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F4A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F4A)

(-) Exons   (0, 0)

(no "Exon" information available for 4F4A)

(-) 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:150
                                                                                                                                                                                      
               SCOP domains d4f4aa_ A: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f4a A   2 PSERTFIAVKPDGVQRNLVGEIIKRFENKGYKLVGLKLLQPTEEQAKQHYIDLASKPFYSGLVSYFSSGPIVGMVWEGLGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVESAKREIAFWFKAEELVSWTSHSVKQIYE 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151


Chain B from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains d4f4ab_ B: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f4a B   2 PSERTFIAVKPDGVQRNLVGEIIKRFENKGYKLVGLKLLQPTEEQAKQHYIDLASKPFYSGLVSYFSSGPIVGMVWEGLGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVESAKREIAFWFKAEELVSWTSHSVKQIYE 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151


Chain C from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains d4f4ac_ C: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f4a C   1 MPSERTFIAVKPDGVQRNLVGEIIKRFENKGYKLVGLKLLQPTEEQAKQHYIDLASKPFYSGLVSYFSSGPIVGMVWEGLGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVESAKREIAFWFKAEELVSWTSHSVKQIYER 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   Legend:   → Mismatch (orange background)
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  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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F4A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F4A)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/TrEMBL
        Q381H3_TRYB2 | Q381H3: 4f36 4fkx 4fky

(-) Related Entries Specified in the PDB File

4f36 APO FORM RELATED ID: SSGCID-TRBRA.00438.A RELATED DB: TARGETTRACK