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(-) Description

Title :  CRYSTAL STRUCTURE OF NTMT1 IN COMPLEX WITH PPKRIA PEPTIDE
 
Authors :  C. Dong, W. Tempel, C. Bountra, C. H. Arrowsmith, A. M. Edwards, J. Min, S Genomics Consortium (Sgc)
Date :  29 Sep 15  (Deposition) - 28 Oct 15  (Release) - 02 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Dong, Y. Mao, W. Tempel, S. Qin, L. Li, P. Loppnau, R. Huang, J. Min
Structural Basis For Substrate Recognition By The Human N-Terminal Methyltransferase 1.
Genes Dev. V. 29 2343 2015
PubMed-ID: 26543161  |  Reference-DOI: 10.1101/GAD.270611.115

(-) Compounds

Molecule 1 - N-TERMINAL XAA-PRO-LYS N-METHYLTRANSFERASE 1
    Chains: A, B
    EC Number: 2.1.1.244
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A-LIC
    Expression System Strain: BL21(DE3)-V3R
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NTMT1, C9ORF32, METTL11A, NRMT, NRMT1, AD-003
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA N-TERMINAL PROTEIN METHYLTRANSFERASE 1A, METHYLTRANSFERASE-LIKE PROTEIN 11A,N-TERMINAL RCC1 METHYLTRANSFERASE, X-PRO-LYS N-TERMINAL PROTEIN METHYLTRANSFERASE 1A,NTM1A
 
Molecule 2 - RCC1
    Chains: D, E
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: SYNTHETIC PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): A D 
Biological Unit 2 (1x):  B E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 48)

Asymmetric Unit (3, 48)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3UNX43Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (3, 26)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3UNX23Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (3, 22)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3UNX20Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:20 , MET A:30 , GLY A:69 , GLY A:71 , ARG A:74 , ILE A:75 , ASP A:91 , ILE A:92 , THR A:93 , PHE A:96 , GLY A:118 , LEU A:119 , GLN A:120 , GLN A:135 , TRP A:136 , VAL A:137 , HIS A:140 , HOH A:434 , HOH A:498 , HOH A:514binding site for residue SAH A 301
2AC2SOFTWARETRP A:136 , VAL A:137 , ILE A:138 , GLY A:139 , ASP A:167 , ASN A:168 , SER A:182 , VAL A:183 , HOH A:448 , HOH A:450 , PRO D:1binding site for residue GOL A 302
3AC3SOFTWAREGLU A:86 , ARG A:112 , HOH A:460 , HOH A:503 , HOH A:512 , ARG B:46binding site for residue GOL A 303
4AC4SOFTWARETRP B:20 , MET B:30 , GLY B:69 , GLY B:71 , ARG B:74 , ILE B:75 , ASP B:91 , ILE B:92 , THR B:93 , PHE B:96 , CYS B:117 , GLY B:118 , LEU B:119 , GLN B:120 , GLN B:135 , TRP B:136 , VAL B:137 , HIS B:140 , HOH B:415 , HOH B:486binding site for residue SAH B 301
5AC5SOFTWARETRP B:136 , VAL B:137 , ILE B:138 , GLY B:139 , ASP B:167 , ASN B:168 , SER B:182 , VAL B:183 , CYS B:184 , HOH B:419 , HOH B:423 , PRO E:1binding site for residue GOL B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E1M)

(-) Cis Peptide Bonds  (1, 2)

Asymmetric Unit
No.Residues
1Gly B:56 -Pro B:57

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E1M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E1M)

(-) Exons   (0, 0)

(no "Exon" information available for 5E1M)

(-) 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:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..hhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhh.........eeeee....hhhhhhh......eeeeee.hhhhhhhhhhhhhhhhh.eeeeee.hhhhh......eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeeeee...eeee....eeeeehhhhhhhhhhh..eeeeeee.........eeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e1m A  -3 VPRGSTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR 223
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       


Chain B from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.hhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhh........eeeee....hhhhhhh......eeeeee.hhhhhhhhhhhhhhhhh.eeeeee.hhhhh......eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeeee....eeee....eeeehhhhhhhhhhhh..eeeeeee.........eeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e1m B  -2 PRGSTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR 223
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217      


Chain D from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5e1m D   1 PPKRIA   6


Chain E from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5e1m E   1 PPKRIA   6
   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 5E1M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E1M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E1M)

(-) Gene Ontology  (34, 38)

Asymmetric Unit(hide GO term definitions)

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  RCC1_HUMAN | P18754
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 Related Entries

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

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        NTM1A_HUMAN | Q9BV86: 2ex4 5cvd 5cve 5e1b 5e1d 5e1o 5e2a 5e2b
        RCC1_HUMAN | P18754: 1a12 1i2m 5e1b 5e1d 5e1o 5e2a 5e2b

(-) Related Entries Specified in the PDB File

5e1b 5e1d 5e1o 5e2a 5e2b