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(-) Description

Title :  CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE B FROM TRYPANOSOMA BRUCEI BOUND TO GTP
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  13 Jun 12  (Deposition) - 27 Jun 12  (Release) - 27 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, African Trypanosomiasis, African Sleeping Sickness, Ntp Biosynthesis, Ndp, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Gardberg, T. E. Edwards, Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of Nucleoside Diphosphate Kinase B From Trypanosma Brucei Bound To Gtp
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: PAVA0421
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TB11.01.7800
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid: 999953
    Strain: 927/4 GUTAT10.1
    Synonym: NDK 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  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1GDP3Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GDP6Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:11 , TYR A:51 , LEU A:54 , PHE A:59 , LEU A:63 , ARG A:87 , THR A:93 , ARG A:104 , VAL A:111 , ASN A:114 , MG A:202 , HOH A:345 , HOH A:357 , HOH A:379 , HOH A:384 , HOH A:385 , HOH A:386 , HOH A:432 , HOH A:433 , HOH A:434 , GLU B:151BINDING SITE FOR RESIDUE GDP A 201
2AC2SOFTWAREGDP A:201 , HOH A:324 , HOH A:345 , HOH A:433 , HOH A:434BINDING SITE FOR RESIDUE MG A 202
3AC3SOFTWARELYS B:11 , TYR B:51 , LEU B:54 , PHE B:59 , LEU B:63 , ARG B:87 , THR B:93 , ARG B:104 , VAL B:111 , ASN B:114 , MG B:202 , HOH B:335 , HOH B:346 , HOH B:355 , HOH B:362 , HOH B:399 , HOH B:401 , HOH B:402 , HOH B:403 , HOH B:420 , HOH B:445 , GLU C:151BINDING SITE FOR RESIDUE GDP B 201
4AC4SOFTWAREGDP B:201 , HOH B:399 , HOH B:401 , HOH B:402 , HOH B:403BINDING SITE FOR RESIDUE MG B 202
5AC5SOFTWAREGLN B:49 , HIS B:50 , GLU B:128BINDING SITE FOR RESIDUE MPD B 203
6AC6SOFTWAREGLU A:151 , LYS 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:301 , HOH C:359 , HOH C:370 , HOH C:397 , HOH C:412 , HOH C:413 , HOH C:414 , HOH C:415 , HOH C:416 , HOH C:418 , HOH C:432 , HOH C:434 , HOH C:478BINDING SITE FOR RESIDUE GDP C 201
7AC7SOFTWAREGDP C:201 , HOH C:412 , HOH C:413 , HOH C:414 , HOH C:415BINDING SITE FOR RESIDUE MG C 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FKY)

(-) 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:152
                                                                                                                                                                                        
               SCOP domains d4fkya_ 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.......eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fky A   1 MPSERTFIAVKPDGVQRNLVGEIIKRFENKGYKLVGLKLLQPTEEQAKQHYIDLASKPFYSGLVSYFSSGPIVGMVWEGLGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVESAKREIAFWFKAEELVSWTSHSVKQIYER 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  


Chain B from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains d4fkyb_ 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.......eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fky B   1 MPSERTFIAVKPDGVQRNLVGEIIKRFENKGYKLVGLKLLQPTEEQAKQHYIDLASKPFYSGLVSYFSSGPIVGMVWEGLGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVESAKREIAFWFKAEELVSWTSHSVKQIYER 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  


Chain C from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains d4fkyc_ 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
                 4fky C   1 MPSERTFIAVKPDGVQRNLVGEIIKRFENKGYKLVGLKLLQPTEEQAKQHYIDLASKPFYSGLVSYFSSGPIVGMVWEGLGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVESAKREIAFWFKAEELVSWTSHSVKQIYERA 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
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  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 4FKY)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

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 Related Entries

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UniProtKB/TrEMBL
        Q381H3_TRYB2 | Q381H3: 4f36 4f4a 4fkx

(-) Related Entries Specified in the PDB File

4f36 APO
4f4a UDP BOUND FORM
4fkx CDP BOUND FORM RELATED ID: SSGCID-TRBRA.00438.A RELATED DB: TARGETTRACK