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(-) Description

Title :  DTDP-FUC3N AND 5-N-FORMYL-THF
 
Authors :  J. B. Thoden, M. -F. Goneau, M. Gilbert, H. M. Holden
Date :  30 Jul 13  (Deposition) - 14 Aug 13  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Fmt, Formyltransferase, N-10-Formyl-Thf, Formylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. B. Thoden, M. F. Goneau, M. Gilbert, H. M. Holden
Structure Of A Sugar N-Formyltransferase From Campylobacter Jejuni.
Biochemistry V. 52 6114 2013
PubMed-ID: 23898784  |  Reference-DOI: 10.1021/BI4009006

(-) Compounds

Molecule 1 - WLARD, A SUGAR 3N-FORMYL TRANSFERASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainROSETTA2(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneC8J_1081
    Organism ScientificCAMPYLOBACTER JEJUNI SUBSP. JEJUNI
    Organism Taxid407148
    Strain81116

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 19)

Asymmetric Unit (6, 19)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO10Ligand/Ion1,2-ETHANEDIOL
3FON2Ligand/IonN-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC ACID
4MPO2Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID
5SO41Ligand/IonSULFATE ION
6T3F2Ligand/Ion(3R,4S,5R,6R)-4-AMINO-3,5-DIHYDROXY-6-METHYLOXAN-2-YL][HYDROXY-[[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXOPYRIMIDIN-1-YL)OXOLAN-2-YL]METHOXY]PHOSPHORYL]HYDROGEN PHOSPHATE
Biological Unit 1 (5, 17)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO10Ligand/Ion1,2-ETHANEDIOL
3FON2Ligand/IonN-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC ACID
4MPO2Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID
5SO41Ligand/IonSULFATE ION
6T3F2Ligand/Ion(3R,4S,5R,6R)-4-AMINO-3,5-DIHYDROXY-6-METHYLOXAN-2-YL][HYDROXY-[[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXOPYRIMIDIN-1-YL)OXOLAN-2-YL]METHOXY]PHOSPHORYL]HYDROGEN PHOSPHATE
Biological Unit 2 (5, 9)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3FON1Ligand/IonN-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC ACID
4MPO1Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID
5SO41Ligand/IonSULFATE ION
6T3F1Ligand/Ion(3R,4S,5R,6R)-4-AMINO-3,5-DIHYDROXY-6-METHYLOXAN-2-YL][HYDROXY-[[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXOPYRIMIDIN-1-YL)OXOLAN-2-YL]METHOXY]PHOSPHORYL]HYDROGEN PHOSPHATE
Biological Unit 3 (4, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3FON1Ligand/IonN-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC ACID
4MPO1Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID
5SO4-1Ligand/IonSULFATE ION
6T3F1Ligand/Ion(3R,4S,5R,6R)-4-AMINO-3,5-DIHYDROXY-6-METHYLOXAN-2-YL][HYDROXY-[[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXOPYRIMIDIN-1-YL)OXOLAN-2-YL]METHOXY]PHOSPHORYL]HYDROGEN PHOSPHATE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:75 , PHE A:78 , ASP A:79 , GLN A:80 , ILE A:81 , ILE A:82 , ASN A:94 , VAL A:106 , ILE A:127 , ASP A:128 , GLY A:130 , ASP A:132 , SER A:191 , ARG A:192 , T3F A:303 , HOH A:406 , HOH A:417 , HOH A:428 , HOH A:461 , HOH A:491 , HOH A:741 , HOH A:797 , EDO B:304BINDING SITE FOR RESIDUE FON A 301
02AC2SOFTWAREPHE A:203 , ILE A:227 , ASN A:228 , PHE A:247 , HOH A:504 , HOH A:592 , HOH A:765 , HOH A:808BINDING SITE FOR RESIDUE MPO A 302
03AC3SOFTWARELYS A:9 , GLU A:77 , PHE A:78 , GLY A:105 , PHE A:107 , THR A:108 , SER A:109 , TYR A:154 , ARG A:192 , LEU A:197 , PHE A:219 , TYR A:222 , GLN A:223 , FON A:301 , HOH A:402 , HOH A:411 , HOH A:413 , HOH A:460 , HOH A:484 , HOH A:487 , HOH A:599 , HOH A:665 , HOH A:749BINDING SITE FOR RESIDUE T3F A 303
04AC4SOFTWARELYS A:204 , ASN A:245 , ILE A:259 , HOH A:481 , FON B:301BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWAREASP A:90 , ARG A:126 , ASN A:175 , TYR A:177 , HOH A:812BINDING SITE FOR RESIDUE EDO A 305
06AC6SOFTWAREILE A:84 , ARG A:126 , ILE A:127 , ASP A:128 , HOH A:445 , HOH A:630 , HOH A:872BINDING SITE FOR RESIDUE EDO A 306
07AC7SOFTWAREASP A:38 , LYS A:39 , ILE A:41 , GLN A:45 , HOH A:473 , HOH A:662 , HOH A:739 , HOH A:755BINDING SITE FOR RESIDUE EDO A 307
08AC8SOFTWAREASP A:194 , ILE A:195 , ASN A:196 , HIS A:199 , HOH A:488 , HOH A:791 , HOH A:802 , HOH A:836BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWAREGLN A:70 , LYS A:88BINDING SITE FOR RESIDUE CL A 309
10BC1SOFTWARELYS A:9 , ASN A:35 , ASN A:37 , HOH A:806BINDING SITE FOR RESIDUE CL A 310
11BC2SOFTWAREASN A:175 , TYR A:177BINDING SITE FOR RESIDUE SO4 A 311
12BC3SOFTWAREEDO A:304 , SER B:75 , PHE B:78 , GLN B:80 , ILE B:81 , ILE B:82 , ASN B:94 , VAL B:106 , ILE B:127 , ASP B:128 , GLY B:130 , ASP B:132 , SER B:191 , ARG B:192 , T3F B:303 , HOH B:433 , HOH B:436 , HOH B:459 , HOH B:466 , HOH B:685BINDING SITE FOR RESIDUE FON B 301
13BC4SOFTWAREPHE B:203 , ILE B:227 , ASN B:228 , PHE B:247 , HOH B:472 , HOH B:485 , HOH B:549 , HOH B:664BINDING SITE FOR RESIDUE MPO B 302
14BC5SOFTWARELYS B:9 , GLU B:77 , PHE B:78 , GLY B:105 , PHE B:107 , THR B:108 , SER B:109 , TYR B:154 , ARG B:192 , LEU B:197 , PHE B:219 , TYR B:222 , GLN B:223 , FON B:301 , HOH B:401 , HOH B:414 , HOH B:440 , HOH B:454 , HOH B:501 , HOH B:503 , HOH B:566 , HOH B:597 , HOH B:655 , HOH B:666BINDING SITE FOR RESIDUE T3F B 303
15BC6SOFTWAREFON A:301 , LYS B:204 , ASN B:245 , ILE B:259 , HOH B:412BINDING SITE FOR RESIDUE EDO B 304
16BC7SOFTWAREASN A:115 , ASN A:116 , TYR B:103 , SER B:188 , HOH B:471BINDING SITE FOR RESIDUE EDO B 305
17BC8SOFTWARETRP B:44 , ARG B:151 , LEU B:269 , LYS B:271 , HOH B:613BINDING SITE FOR RESIDUE EDO B 306
18BC9SOFTWAREASN B:11 , ASN B:15 , LYS B:46 , ASP B:63 , ASN B:252 , ASN B:270BINDING SITE FOR RESIDUE EDO B 307
19CC1SOFTWAREASP B:194 , ILE B:195 , ASN B:196 , HIS B:199 , HOH B:476 , HOH B:603 , HOH B:783BINDING SITE FOR RESIDUE EDO B 308

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:100 -Pro A:101
2Leu B:100 -Pro B:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LXU)

(-) 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:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeehhhhhhhhhhhhhhhh.hhh.eeeee............hhhhhhhhh..ee.hhhhh......eeeee......hhhhh...eeeeee.......ee....hhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..............eehhhhh..........hhhhhhhhhhh.........ee..eeeeeeeeeeee.....eee...eeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lxu A  -1 GHMIKICIAGKNNIAVNSLQFILKNYFEADQIVVIPNKNDKGIDSWQKSLLKFALDNNIKIVTLDEIYNIEQIIFFSLEFDQIIKIENFKSDRLFNIHFSALPKYKGVFTSITPILNNELESGVTLHRIDNGIDTGNIIDQHCFPIDINDTARDLYFNYLKYGESIFKKNIQTIINNSYKDLKQTNINSSYFSRKDINLVHKINFKKTSFEIHNQIRAFIFQEYQLPIINNSKIIKSILANEFIGYNVFEEFENYFIISGIDGFKIIAQKLNK 271
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268   

Chain B from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeehhhhhhhhhhhhhhhh.hhh.eeeee............hhhhhhhhh..ee............eeeee......hhhhh....eeeee.......ee....hhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..............eehhhhh..........hhhhhhhhhhh.........ee..eeeeeeeeeeee.....eee...eeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lxu B  -1 GHMIKICIAGKNNIAVNSLQFILKNYFEADQIVVIPNKNDKGIDSWQKSLLKFALDNNIKIVTLDEIYNIEQIIFFSLEFDQIIKIENFKSDRLFNIHFSALPKYKGVFTSITPILNNELESGVTLHRIDNGIDTGNIIDQHCFPIDINDTARDLYFNYLKYGESIFKKNIQTIINNSYKDLKQTNINSSYFSRKDINLVHKINFKKTSFEIHNQIRAFIFQEYQLPIINNSKIIKSILANEFIGYNVFEEFENYFIISGIDGFKIIAQKLNKL 272
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268    

   Legend:   → Mismatch (orange background)
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    → 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 4LXU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4LXU)

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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4LXU)

(-) Related Entries Specified in the PDB File

4lxq SAME PROTEIN IN COMPLEX WITH DTPD AND 5-N-FORMYL-THF
4lxt SAME PROTEIN IN COMPLEX WITH DTPD-QUI3N AND 5-N-FORMYL-THF
4lxx
4lxy
4ly0
4ly3