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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ALKYLHYDROPEROXIDE REDUCTASE AHPF FROM ESCHERICHIA COLI
 
Authors :  P. V. Dip, N. Kamariah, M. S. S. Manimekalai, A. M. Balakrishna, G. Grube
Date :  20 Dec 13  (Deposition) - 05 Nov 14  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. V. Dip, N. Kamariah, M. S. Subramanian Manimekalai, W. Nartey, A. M. Balakrishna, F. Eisenhaber, B. Eisenhaber, G. Gruber
Structure, Mechanism And Ensemble Formation Of The Alkylhydroperoxide Reductase Subunits Ahpc And Ahpf From Escherichia Coli
Acta Crystallogr. , Sect. D V. 70 2848 2014
PubMed-ID: 25372677  |  Reference-DOI: 10.1107/S1399004714019233
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALKYL HYDROPEROXIDE REDUCTASE SUBUNIT F
    Chains: A
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: ALKYL HYDROPEROXIDE REDUCTASE F52A PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 25)

Asymmetric Unit (7, 25)
No.NameCountTypeFull Name
1CD1Ligand/IonCADMIUM ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL7Ligand/IonGLYCEROL
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5PGE6Ligand/IonTRIETHYLENE GLYCOL
6SO48Ligand/IonSULFATE ION
7TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (6, 48)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL14Ligand/IonGLYCEROL
4PG42Ligand/IonTETRAETHYLENE GLYCOL
5PGE12Ligand/IonTRIETHYLENE GLYCOL
6SO416Ligand/IonSULFATE ION
7TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:219 , GLY A:221 , PRO A:222 , ALA A:223 , GLY A:242 , GLU A:243 , ARG A:244 , GLY A:247 , GLN A:248 , THR A:252 , ASN A:257 , GLN A:288 , SER A:289 , ALA A:290 , ALA A:321 , THR A:322 , GLY A:323 , CYS A:348 , ASN A:454 , TRP A:457 , GLY A:487 , ASP A:488 , LYS A:495 , GLN A:496 , ILE A:497 , ALA A:500 , GOL A:619 , HOH A:701 , HOH A:702 , HOH A:736 , HOH A:738 , HOH A:739 , HOH A:747 , HOH A:748 , HOH A:753 , HOH A:814 , HOH A:834BINDING SITE FOR RESIDUE FAD A 601
02AC2SOFTWAREALA A:105 , GLN A:106 , SER A:107 , SER A:126 , SER A:128 , HOH A:930 , HOH A:1084 , HOH A:1085BINDING SITE FOR RESIDUE SO4 A 602
03AC3SOFTWAREGLY A:364 , ASN A:365 , SER A:366 , PGE A:621 , HOH A:785BINDING SITE FOR RESIDUE SO4 A 603
04AC4SOFTWAREPRO A:453 , ASN A:454 , THR A:455 , ASN A:456 , TRP A:457 , HOH A:774 , HOH A:834 , HOH A:918 , HOH A:1117BINDING SITE FOR RESIDUE SO4 A 604
05AC5SOFTWAREPRO A:332 , GLY A:333 , GLU A:334 , ASP A:335 , GLN A:336 , HOH A:865 , HOH A:902 , HOH A:903BINDING SITE FOR RESIDUE SO4 A 605
06AC6SOFTWAREARG A:357 , HIS A:380 , HOH A:789 , HOH A:1141BINDING SITE FOR RESIDUE SO4 A 606
07AC7SOFTWAREHIS A:438 , ASN A:439 , HOH A:802 , HOH A:842 , HOH A:1022BINDING SITE FOR RESIDUE SO4 A 607
08AC8SOFTWARESER A:30 , ALA A:31 , HOH A:812 , HOH A:958 , HOH A:1178BINDING SITE FOR RESIDUE SO4 A 608
09AC9SOFTWAREASP A:473 , ALA A:474 , HOH A:1064 , HOH A:1105BINDING SITE FOR RESIDUE SO4 A 609
10BC1SOFTWAREASN A:439 , GLU A:459 , GLY A:460 , ALA A:461 , GLU A:463 , ASN A:479 , HOH A:915 , HOH A:1022BINDING SITE FOR RESIDUE PGE A 610
11BC2SOFTWAREILE A:471 , GLU A:477 , THR A:478 , ASN A:479 , HOH A:922 , HOH A:1131 , HOH A:1138BINDING SITE FOR RESIDUE PGE A 611
12BC3SOFTWAREILE A:236 , ILE A:372 , LYS A:519 , HOH A:1101BINDING SITE FOR RESIDUE PGE A 612
13BC4SOFTWAREHIS A:100 , PRO A:101 , SER A:102 , GLN A:106 , ASN A:131 , LEU A:145 , HOH A:1100 , HOH A:1114BINDING SITE FOR RESIDUE GOL A 613
14BC5SOFTWAREHIS A:85 , GLU A:110 , HIS A:114 , HIS A:130 , HOH A:1046BINDING SITE FOR RESIDUE CD A 614
15BC6SOFTWAREARG A:233 , GLY A:235 , LYS A:354 , HOH A:1191BINDING SITE FOR RESIDUE GOL A 615
16BC7SOFTWAREGLU A:477 , THR A:478 , ASN A:479 , LYS A:481 , GOL A:625 , HOH A:921BINDING SITE FOR RESIDUE PGE A 616
17BC8SOFTWAREPHE A:245 , LYS A:274 , HOH A:813 , HOH A:1017BINDING SITE FOR RESIDUE PG4 A 617
18BC9SOFTWAREGLU A:104 , GLY A:156 , GLN A:160 , MET A:169 , HOH A:930 , HOH A:1086BINDING SITE FOR RESIDUE PGE A 618
19CC1SOFTWARETHR A:252 , VAL A:253 , ASP A:254 , THR A:339 , ASP A:349 , FAD A:601 , HOH A:702 , HOH A:703 , HOH A:815 , HOH A:1183BINDING SITE FOR RESIDUE GOL A 619
20CC2SOFTWAREGLU A:416 , ASN A:465 , ARG A:466 , HOH A:714 , HOH A:923 , HOH A:1147BINDING SITE FOR RESIDUE TRS A 620
21CC3SOFTWAREARG A:327 , SER A:366 , VAL A:447 , GLN A:448 , ILE A:449 , GLY A:450 , LEU A:451 , SO4 A:603BINDING SITE FOR RESIDUE PGE A 621
22CC4SOFTWAREGLY A:341 , PHE A:353 , HOH A:706 , HOH A:1182BINDING SITE FOR RESIDUE GOL A 622
23CC5SOFTWAREASP A:335 , GLN A:336 , ARG A:338 , LYS A:340 , LYS A:391 , HOH A:1119BINDING SITE FOR RESIDUE GOL A 623
24CC6SOFTWAREASP A:28 , ALA A:34 , LYS A:37 , GLU A:54 , GLY A:300 , ARG A:316 , THR A:518 , ALA A:521BINDING SITE FOR RESIDUE GOL A 624
25CC7SOFTWAREGLU A:299 , LYS A:481 , ARG A:517 , THR A:518 , PGE A:616 , HOH A:837 , HOH A:1129BINDING SITE FOR RESIDUE GOL A 625

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:345 -A:348

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:62 -Pro A:63
2Val A:171 -Pro A:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O5Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O5Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4O5Q)

(-) 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:521
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhhhhhh....eeeee.........eeeee........eee...hhhhhhhhhhhhhhhh......hhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh......eeee..eeeee...hhhhhhhhhh.....hhhhhhhh.....eeee..hhhhhhhhhhhhhh...eeeee...hhhhhhh.ee........eehhhhhhhhhhhhhh...eeee...eeeee........eeeee....eeee..eee...eee......hhhhhh...ee.hhhhhhhhhh..eeeee..hhhhhhhhhhhhh...eeeee........hhhhhhhhhh...eeee..eeeeeeee....eeeeeeee.....eeeee..eeee...eee.hhhhh.......................eee..........hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o5q A   1 MLDTNMKTQLKAYLEKLTKPVELIATLDDSAKSAEIKELLAEIAELSDKVTFKEDNSLPVRKPSFLITNPGSNQGPRFAGSPLGHEFTSLVLALLWTGGHPSKEAQSLLEQIRHIDGDFEFETYYSLSCHNCPDVVQALNLMSVLNPRIKHTAIDGGTFQNEITDRNVMGVPAVFVNGKEFGQGRMTLTEIVAKIDTGAEKRAAEELNKRDAYDVLIVGSGPAGAAAAIYSARKGIRTGLMGERFGGQILDTVDIENYISVPKTEGQKLAGALKVHVDEYDVDVIDSQSASKLIPAAVEGGLHQIETASGAVLKARSIIVATGAKWRNMNVPGEDQYRTKGVTYCPHCDGPLFKGKRVAVIGGGNSGVEAAIDLAGIVEHVTLLEFAPEMKADQVLQDKLRSLKNVDIILNAQTTEVKGDGSKVVGLEYRDRVSGDIHNIELAGIFVQIGLLPNTNWLEGAVERNRMGEIIIDAKCETNVKGVFAAGDCTTVPYKQIIIATGEGAKASLSAFDYLIRTKTA 521
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520
   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 4O5Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O5Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O5Q)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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  AHPF_ECOLI | P35340
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        AHPF_ECOLI | P35340: 1fl2 4o5u 4xvg 4ykf 4ykg

(-) Related Entries Specified in the PDB File

1fl2 4o5r 4o5u