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(-) Description

Title :  STRUCTURE OF THE NTF2:RANGDP COMPLEX
 
Authors :  M. Stewart
Date :  09 Jun 15  (Deposition) - 01 Jul 15  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Nuclear Transport, Rangdp, Ntf2, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Stewart, H. M. Kent, A. J. Mccoy
Structural Basis For Molecular Recognition Between Nuclear Transport Factor 2 (Ntf2) And The Gdp-Bound Form Of The Ras-Family Gtpase Ran.
J. Mol. Biol. V. 277 635 1998
PubMed-ID: 9533885

(-) Compounds

Molecule 1 - NUCLEAR TRANSPORT FACTOR 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NUTF2, NTF2
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: NTF-2
 
Molecule 2 - GTP-BINDING NUCLEAR PROTEIN RAN
    Chains: C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RAN
    Organism Common: DOG
    Organism Scientific: CANIS FAMILIARIS
    Organism Taxid: 9615
    Synonym: GTPASE RAN,RAS-LIKE PROTEIN TC4,RAS-RELATED NUCLEAR PROTEIN

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1GDP3Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY C:20 , THR C:21 , GLY C:22 , LYS C:23 , THR C:24 , THR C:25 , GLU C:70 , ASN C:122 , LYS C:123 , ASP C:125 , ILE C:126 , SER C:150 , ALA C:151 , LYS C:152 , MG C:302 , HOH C:418 , HOH C:428 , HOH C:433 , HOH C:435binding site for residue GDP C 301
2AC2SOFTWARETHR C:24 , GDP C:301 , HOH C:418 , HOH C:424 , HOH C:428 , HOH C:435binding site for residue MG C 302
3AC3SOFTWAREGLY D:19 , GLY D:20 , THR D:21 , GLY D:22 , LYS D:23 , THR D:24 , THR D:25 , ASN D:122 , LYS D:123 , ASP D:125 , ILE D:126 , SER D:150 , ALA D:151 , LYS D:152 , MG D:302 , HOH D:412 , HOH D:416 , HOH D:434binding site for residue GDP D 301
4AC4SOFTWARETHR D:24 , GDP D:301 , HOH D:412 , HOH D:425 , HOH D:427 , HOH D:434binding site for residue MG D 302
5AC5SOFTWARETHR E:24 , GDP E:303 , HOH E:401 , HOH E:412 , HOH E:421 , HOH E:427binding site for residue MG E 301
6AC6SOFTWARETHR D:32 , PRO D:180 , ALA D:181 , HOH D:452 , THR E:32 , PRO E:180 , ALA E:181 , HOH E:417 , HOH E:420 , HOH E:449 , HOH E:450binding site for residue SO4 E 302
7AC7SOFTWAREGLY E:20 , THR E:21 , GLY E:22 , LYS E:23 , THR E:24 , THR E:25 , GLU E:70 , ASN E:122 , LYS E:123 , ASP E:125 , ILE E:126 , ALA E:151 , LYS E:152 , MG E:301 , HOH E:401 , HOH E:415 , HOH E:421 , HOH E:457binding site for residue GDP E 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BXQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5BXQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BXQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BXQ)

(-) Exons   (0, 0)

(no "Exon" information available for 5BXQ)

(-) Sequences/Alignments

Asymmetric/Biological 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:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeehhhhhhhhhhh.....eeeeeeeeeeee.....eeeeeeeeeee.....eeeeeeeeeeee..eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxq A   4 KPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMFRLALHNFG 127
                                    13        23        33        43        53        63        73        83        93       103       113       123    


Chain B from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee..eeeehhhhhhhhhhh.....eeeeeeeeeeee.....eeeeeeeeeee.....eeeeeeeeeee....eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxq B   4 KPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMFRLALHNFG 127
                                    13        23        33        43        53        63        73        83        93       103       113       123    


Chain C from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhhhhh.eee....eeeeeeeeee..eeeeeeeeee.hhhhh...hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeee.........hhhhhh.eeeee.hhhhh...hhhhhhhhhhhhh...................hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5bxq C   8 QVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVA 204
                                    17        27        37        47        57        67        77        87        97       107       117       127       137|      152       162       172       182       192       202  
                                                                                                                                                           137|                                                             
                                                                                                                                                            143                                                             


Chain D from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee....hhhhhhh.hhhhhhh.eee....eeeeeeeeee..eeeeeeeeee.hhhhh...hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeee.........hhhhhh..eeeee.hhhhh...hhhhhhhhhhhhh.....eee...........hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5bxq D   7 PQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTA 208
                                    16        26        36        46        56        66        76        86        96       106       116       126       136 ||    150       160       170       180       190       200        
                                                                                                                                                             138|                                                                 
                                                                                                                                                              143                                                                 


Chain E from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhh.hhhhhhh.eeehhh.eeeeeeeeee..eeeeeeeeee.hhhhhh..hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeee...................eeeee.hhhhh...hhhhhhhhhhhhh.....eee...........hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxq E   8 QVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDE 212
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  ||   149       159       169       179       189       199       209   
                                                                                                                                                              140|                                                                     
                                                                                                                                                               143
   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 ; only for superseded entry 1A2K: 2,5)

(no "SCOP Domain" information available for 5BXQ, only for superseded entry 1A2K replaced by 5BXQ)

(-) CATH Domains  (0, 0 ; only for superseded entry 1A2K: 2,5)

(no "CATH Domain" information available for 5BXQ, only for superseded entry 1A2K replaced by 5BXQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BXQ)

(-) Gene Ontology  (27, 30)

Asymmetric/Biological Unit(hide GO term definitions)

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  5bxq
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  RAN_CANLF | P62825
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 Related Entries

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

UniProtKB/Swiss-Prot
        NTF2_RAT | P61972: 1a2k 1ar0 1ask 1gy5 1gy6 1jb2 1jb4 1jb5 1oun 1qma 1u5o
        RAN_CANLF | P62825: 1a2k 1byu 1qg2 1qg4 1wa5 2bku 3a6p 3ran 3w3z

(-) Related Entries Specified in the PDB File

1a2k RE-REFINEMENT TO REPLACE 1A2K