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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 6-ETHYL-5-[(3S)-3-[3-METHOXY-5-(PYRIDINE-4-YL)PHENYL]BUT-1-YN-1-YL]PYRIMIDINE-2,4-DIAMINE (UCP1006)
 
Authors :  K. M. Lamb, A. C. Anderson
Date :  22 Apr 13  (Deposition) - 09 Oct 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase, 5, 6, 7, 8-Tetrahydrofolate; Nadp+; 7, 8-Dihydrofolate, Hydride Shift, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Lamb, N. G-Dayanandan, D. L. Wright, A. C. Anderson
Elucidating Features That Drive The Design Of Selective Antifolates Using Crystal Structures Of Human Dihydrofolate Reductase.
Biochemistry V. 52 7318 2013
PubMed-ID: 24053334  |  Reference-DOI: 10.1021/BI400852H

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: A, B
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET41A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DHFR, HUDHFR
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Strain: RP11-399L5

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
106U2Ligand/Ion6-ETHYL-5-{(3R)-3-[3-METHOXY-5-(PYRIDIN-4-YL)PHENYL]BUT-1-YN-1-YL}PYRIMIDINE-2,4-DIAMINE
2CA4Ligand/IonCALCIUM ION
3EOH5Ligand/IonETHANOL
4NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
106U1Ligand/Ion6-ETHYL-5-{(3R)-3-[3-METHOXY-5-(PYRIDIN-4-YL)PHENYL]BUT-1-YN-1-YL}PYRIMIDINE-2,4-DIAMINE
2CA-1Ligand/IonCALCIUM ION
3EOH3Ligand/IonETHANOL
4NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
106U1Ligand/Ion6-ETHYL-5-{(3R)-3-[3-METHOXY-5-(PYRIDIN-4-YL)PHENYL]BUT-1-YN-1-YL}PYRIMIDINE-2,4-DIAMINE
2CA-1Ligand/IonCALCIUM ION
3EOH2Ligand/IonETHANOL
4NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:8 , ALA A:9 , ILE A:16 , GLY A:17 , GLY A:20 , ASP A:21 , LEU A:22 , GLY A:53 , LYS A:54 , LYS A:55 , THR A:56 , SER A:59 , LEU A:75 , SER A:76 , ARG A:77 , GLU A:78 , ARG A:91 , VAL A:115 , GLY A:117 , SER A:118 , SER A:119 , VAL A:120 , TYR A:121 , GLU A:123 , THR A:146 , 06U A:202 , HOH A:326 , HOH A:372 , HOH A:416BINDING SITE FOR RESIDUE NDP A 201
02AC2SOFTWAREILE A:7 , VAL A:8 , ALA A:9 , ASP A:21 , GLU A:30 , PHE A:31 , PHE A:34 , SER A:59 , PRO A:61 , ASN A:64 , LEU A:67 , VAL A:115 , TYR A:121 , THR A:136 , NDP A:201 , HOH A:454BINDING SITE FOR RESIDUE 06U A 202
03AC3SOFTWAREASP A:21 , LEU A:22 , TRP A:24 , HOH A:380 , GLU B:161BINDING SITE FOR RESIDUE EOH A 203
04AC4SOFTWAREGLY A:2 , GLU B:171BINDING SITE FOR RESIDUE EOH A 204
05AC5SOFTWAREGLN A:47 , LYS A:68 , GLY A:69BINDING SITE FOR RESIDUE EOH A 205
06AC6SOFTWARESER A:3 , ASN A:5 , LYS A:132 , HOH A:381 , HOH A:438BINDING SITE FOR RESIDUE CA A 206
07AC7SOFTWAREVAL B:8 , ALA B:9 , ILE B:16 , GLY B:17 , GLY B:20 , ASP B:21 , TRP B:24 , GLY B:53 , LYS B:54 , LYS B:55 , THR B:56 , SER B:59 , LEU B:75 , SER B:76 , ARG B:77 , GLU B:78 , ARG B:91 , VAL B:115 , GLY B:117 , SER B:118 , SER B:119 , VAL B:120 , GLU B:123 , THR B:146 , 06U B:202 , HOH B:309 , HOH B:320 , HOH B:395 , HOH B:409 , HOH B:414BINDING SITE FOR RESIDUE NDP B 201
08AC8SOFTWAREILE B:7 , VAL B:8 , ALA B:9 , ASP B:21 , GLU B:30 , PHE B:31 , PHE B:34 , SER B:59 , PRO B:61 , ASN B:64 , VAL B:115 , THR B:136 , NDP B:201BINDING SITE FOR RESIDUE 06U B 202
09AC9SOFTWARELYS A:157 , PRO B:61 , GLU B:62BINDING SITE FOR RESIDUE EOH B 203
10BC1SOFTWAREGLU A:62 , LYS B:157BINDING SITE FOR RESIDUE EOH B 204
11BC2SOFTWAREARG B:32 , HOH B:390 , HOH B:428 , HOH B:438BINDING SITE FOR RESIDUE CA B 205
12BC3SOFTWAREVAL B:10 , GLN B:12 , ARG B:137 , ILE B:138 , HOH B:317 , HOH B:380BINDING SITE FOR RESIDUE CA B 206
13BC4SOFTWAREPRO A:25 , LYS A:173 , HOH A:383 , TYR B:162 , GLU B:183 , HOH B:388BINDING SITE FOR RESIDUE CA B 207

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:65 -Pro A:66
2Gly A:116 -Gly A:117
3Arg B:65 -Pro B:66
4Gly B:116 -Gly B:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KAK)

(-) 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:186
                                                                                                                                                                                                                          
               SCOP domains d4kaka_ A: Dihydrofolate reductases, eukaryotic type                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee....eee.........hhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhh.....eeeee............eee.hhhhhhhhh........eeeeee..hhhhhhhhhh...eeeeeeeee.......ee.........ee...........eee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kak A   1 VGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND 186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      


Chain B from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains d4kakb_ B: Dihydrofolate reductases, eukaryotic type                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee....eee.........hhhhhhhhhhhhhh......eeeeeehhhhhhhhhhhhh.....eeeee............eee.hhhhhhhhh........eeeeee..hhhhhhhhhh...eeeeeeeee.......ee.........ee...........eee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kak B   1 VGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND 186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  1.5.1.3
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(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DYR_HUMAN | P00374: 1boz 1dhf 1dlr 1dls 1drf 1hfp 1hfq 1hfr 1kms 1kmv 1mvs 1mvt 1ohj 1ohk 1pd8 1pd9 1pdb 1s3u 1s3v 1s3w 1u71 1u72 1yho 2c2s 2c2t 2dhf 2w3a 2w3b 2w3m 3eig 3f8y 3f8z 3f91 3fs6 3ghc 3ghv 3ghw 3gi2 3gyf 3l3r 3n0h 3ntz 3nu0 3nxo 3nxr 3nxt 3nxv 3nxx 3nxy 3nzd 3oaf 3s3v 3s7a 4ddr 4g95 4kbn 4kd7 4keb 4kfj 4m6j 4m6k 4m6l 4qhv 4qjc 5hpb 5hqy 5hqz 5hsr 5hsu 5ht4 5ht5 5hui 5hvb 5hve

(-) Related Entries Specified in the PDB File

4kbn 4kd7 4keb 4kfj