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(-) Description

Title :  CRYSTAL STRUCTURE OF FGFR1-Y563C (FGFR4 SURROGATE) COVALENTLY BOUND TO H3B-6527
 
Authors :  J. H. C. Tsai, D. Reynolds, P. Fekkes, P. Smith, N. A. Larsen
Date :  30 Apr 17  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Fgfr4, H3B-56527, Covalent Compound, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. C. Tsai, D. Reynolds, P. Fekkes, P. Smith, N. A. Larsen
Crystal Structure Of Fgfr1-Y563C (Fgfr4 Surrogate) Covalently Bound To H3B-6527
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FIBROBLAST GROWTH FACTOR RECEPTOR 1
    Chains: A, B
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DE3 STAR
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 458-765
    Gene: FGFR1, BFGFR, CEK, FGFBR, FLG, FLT2, HBGFR
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FGFR-1,BASIC FIBROBLAST GROWTH FACTOR RECEPTOR 1,BFGF-R-1, FMS-LIKE TYROSINE KINASE 2,FLT-2,N-SAM,PROTO-ONCOGENE C-FGR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric Unit (3, 21)
No.NameCountTypeFull Name
19ES2Ligand/IonN-{2-[(6-{[(2,6-DICHLORO-3,5-DIMETHOXYPHENYL)CARBAMOYL](METHYL)AMINO}PYRIMIDIN-4-YL)AMINO]-5-(4-ETHYLPIPERAZIN-1-YL)PHENYL}PROPANAMIDE
2EDO15Ligand/Ion1,2-ETHANEDIOL
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
19ES1Ligand/IonN-{2-[(6-{[(2,6-DICHLORO-3,5-DIMETHOXYPHENYL)CARBAMOYL](METHYL)AMINO}PYRIMIDIN-4-YL)AMINO]-5-(4-ETHYLPIPERAZIN-1-YL)PHENYL}PROPANAMIDE
2EDO9Ligand/Ion1,2-ETHANEDIOL
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 9)
No.NameCountTypeFull Name
19ES1Ligand/IonN-{2-[(6-{[(2,6-DICHLORO-3,5-DIMETHOXYPHENYL)CARBAMOYL](METHYL)AMINO}PYRIMIDIN-4-YL)AMINO]-5-(4-ETHYLPIPERAZIN-1-YL)PHENYL}PROPANAMIDE
2EDO6Ligand/Ion1,2-ETHANEDIOL
3SO42Ligand/IonSULFATE ION
Biological Unit 3 (3, 21)
No.NameCountTypeFull Name
19ES2Ligand/IonN-{2-[(6-{[(2,6-DICHLORO-3,5-DIMETHOXYPHENYL)CARBAMOYL](METHYL)AMINO}PYRIMIDIN-4-YL)AMINO]-5-(4-ETHYLPIPERAZIN-1-YL)PHENYL}PROPANAMIDE
2EDO15Ligand/Ion1,2-ETHANEDIOL
3SO44Ligand/IonSULFATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:492 , LEU A:494 , ALA A:512 , LYS A:514 , GLU A:531 , VAL A:559 , VAL A:561 , GLU A:562 , ALA A:564 , GLY A:567 , GLU A:571 , ALA A:640 , ASP A:641 , EDO A:806binding site for residue 9ES A 801
02AC2SOFTWARESER A:584 , TYR A:585 , HOH A:944 , HOH A:972 , ARG B:734binding site for residue SO4 A 802
03AC3SOFTWAREARG A:570 , ARG A:627 , THR A:657 , ASN A:659 , ARG A:661 , HOH A:906 , HOH A:912binding site for residue SO4 A 803
04AC4SOFTWARETRP A:684 , TYR A:701 , ARG A:718 , MET A:719 , TRP A:737 , HOH A:911binding site for residue EDO A 804
05AC5SOFTWARETHR A:746 , PHE A:747 , LYS A:748 , HOH A:915 , HOH A:920binding site for residue EDO A 805
06AC6SOFTWAREARG A:627 , ASN A:628 , ASP A:641 , 9ES A:801binding site for residue EDO A 806
07AC7SOFTWAREARG A:577 , GLY A:698 , SER A:699 , HOH A:948binding site for residue EDO A 807
08AC8SOFTWARETHR A:726 , ASN A:727 , GLU A:728binding site for residue EDO A 808
09AC9SOFTWARELYS A:542 , ARG A:609binding site for residue EDO A 809
10AD1SOFTWARELYS A:665 , SER A:699 , GLY A:703 , HOH A:925 , HOH A:947 , HOH A:952binding site for residue EDO A 810
11AD2SOFTWAREPRO A:745 , THR A:746 , GLN A:749 , HOH A:907 , HOH A:936 , ASP B:554 , GLY B:555 , PRO B:556binding site for residue EDO A 811
12AD3SOFTWAREGLU A:708 , LYS A:711 , LEU A:712 , GLU A:715 , GLY B:703 , HOH B:989binding site for residue EDO A 812
13AD4SOFTWAREVAL B:492 , LEU B:494 , LYS B:514 , GLU B:531 , VAL B:559 , VAL B:561 , GLU B:562 , ALA B:564 , GLU B:571 , LEU B:630 , ALA B:640 , ASP B:641 , PHE B:642 , HOH B:936binding site for residue 9ES B 801
14AD5SOFTWAREARG B:570 , ARG B:627 , THR B:657 , ASN B:659 , ARG B:661 , HOH B:917 , HOH B:933binding site for residue SO4 B 802
15AD6SOFTWAREVAL B:601 , PHE B:694 , ASN B:724 , THR B:726 , LEU B:729binding site for residue SO4 B 803
16AD7SOFTWARETRP B:684 , TYR B:701 , ARG B:718 , MET B:719 , TRP B:737 , HOH B:922binding site for residue EDO B 804
17AD8SOFTWAREGLY B:580binding site for residue EDO B 805
18AD9SOFTWAREASP A:735 , HIS A:738 , HOH A:942 , HOH A:984 , LEU B:516 , LYS B:517 , SER B:518 , PRO B:556 , HOH B:901binding site for residue EDO B 806
19AE1SOFTWAREGLU B:728 , ASP B:753 , ARG B:756binding site for residue EDO B 807
20AE2SOFTWAREASP B:735 , GLN B:743 , PRO B:745binding site for residue EDO B 808

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:646 -Asp A:647
2His B:649 -His B:650

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VND)

(-) 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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhh.eeeeeeeee....eeeeeeee.........eeeeeeee......hhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.....................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vnd A 463 YELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVECASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE 765
                                   472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642    || 653       663       673       683       693       703       713       723       733       743       753       763  
                                                                                                                                                                                                                  647|                                                                                                                    
                                                                                                                                                                                                                   649                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhh.eeeeeeeee...eeeeeeeee.........eeeeeeeee....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee......................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vnd B 460 VSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVECASKGNLREYLQARRPPGEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE 765
                                   469       479       489       499       509       519       529       539       549       559       569       579||     600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760     
                                                                                                                                                  580|                                                                                                                                                                             
                                                                                                                                                   592
   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 5VND)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (99, 99)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        FGFR1_HUMAN | P11362: 1agw 1cvs 1evt 1fgi 1fgk 1fq9 1xr0 2cr3 2fgi 3c4f 3dpk 3gqi 3gql 3js2 3krj 3krl 3kxx 3ky2 3ojv 3rhx 3tt0 4f63 4f64 4f65 4nk9 4nka 4nks 4rwi 4rwj 4rwk 4rwl 4uwb 4uwc 4uwy 4v01 4v04 4v05 4wun 4zsa 5a46 5a4c 5am6 5am7 5b7v 5ew8 5flf 5uq0 5ur1

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