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(-) Description

Title :  CRYSTAL STRUCTURE OF NDH WITH TRT
 
Authors :  W. Li, Y. Feng, J. Ge, M. Yang
Date :  19 Jul 12  (Deposition) - 24 Oct 12  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Electron Transfer, Trt, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Feng, W. Li, J. Li, J. Wang, J. Ge, D. Xu, Y. Liu, K. Wu, Q. Zeng, J. W. Wu, C. Tian, B. Zhou, M. Yang
Structural Insight Into The Type-Ii Mitochondrial Nadh Dehydrogenases.
Nature V. 491 478 2012
PubMed-ID: 23086143  |  Reference-DOI: 10.1038/NATURE11541

(-) Compounds

Molecule 1 - ROTENONE-INSENSITIVE NADH-UBIQUINONE OXIDOREDUCTASE, MITOCHONDRIAL
    Chains: A, B
    EC Number: 1.6.5.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NDI1, YML120C, YM7056.06C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: INTERNAL NADH DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MG10Ligand/IonMAGNESIUM ION
3TRT6Ligand/IonFRAGMENT OF TRITON X-100

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:479 , ILE A:480 , PHE A:496 , TRP A:499 , ALA A:503BINDING SITE FOR RESIDUE TRT A 601
02AC2SOFTWARETRP A:63 , GLN A:394 , HIS A:397 , LEU A:444 , GLY A:445 , ALA A:446 , LEU A:447 , MET A:485BINDING SITE FOR RESIDUE TRT A 602
03AC3SOFTWAREGLY A:60 , SER A:61 , GLY A:62 , TRP A:63 , GLY A:64 , ILE A:82 , SER A:83 , PRO A:84 , ARG A:85 , THR A:91 , PRO A:92 , GLU A:128 , ALA A:129 , ALA A:175 , VAL A:176 , GLY A:177 , LEU A:195 , THR A:239 , ARG A:344 , GLY A:382 , ASP A:383 , PRO A:391 , THR A:392 , ALA A:393 , GLN A:394 , ALA A:396 , TYR A:482 , MG A:604 , MG A:605 , MG A:606 , MG A:607 , HOH A:704 , HOH A:726 , HOH A:752 , HOH A:755 , HOH A:895 , HOH A:912BINDING SITE FOR RESIDUE FAD A 603
04AC4SOFTWAREALA A:175 , VAL A:176 , GLY A:177 , ILE A:381 , GLY A:382 , ASP A:383 , ASN A:384 , FAD A:603BINDING SITE FOR RESIDUE MG A 604
05AC5SOFTWAREGLY A:62 , GLY A:64 , ALA A:65 , ALA A:175 , FAD A:603BINDING SITE FOR RESIDUE MG A 605
06AC6SOFTWAREGLY A:62 , ARG A:85 , LEU A:89 , FAD A:603 , HOH A:704BINDING SITE FOR RESIDUE MG A 606
07AC7SOFTWAREGLY A:177 , ALA A:178 , LYS A:196 , ASP A:383 , FAD A:603BINDING SITE FOR RESIDUE MG A 607
08AC8SOFTWAREALA A:489 , LEU A:493 , ILE B:500 , PHE B:504 , TRT B:602BINDING SITE FOR RESIDUE TRT B 601
09AC9SOFTWAREPHE A:505 , ALA B:489 , TRT B:601BINDING SITE FOR RESIDUE TRT B 602
10BC1SOFTWAREARG B:479 , ILE B:480 , PHE B:496 , TRP B:499BINDING SITE FOR RESIDUE TRT B 603
11BC2SOFTWAREGLN B:394 , LEU B:444 , GLY B:445 , ALA B:446 , LEU B:447 , ILE B:459 , MET B:485BINDING SITE FOR RESIDUE TRT B 604
12BC3SOFTWAREGLY B:333 , HOH B:722 , HOH B:785 , HOH B:812 , HOH B:820BINDING SITE FOR RESIDUE MG B 605
13BC4SOFTWARELEU B:116 , LYS B:118 , HOH B:736BINDING SITE FOR RESIDUE MG B 606
14BC5SOFTWAREGLY B:60 , SER B:61 , GLY B:62 , TRP B:63 , GLY B:64 , ILE B:82 , SER B:83 , PRO B:84 , ARG B:85 , THR B:91 , PRO B:92 , GLU B:128 , ALA B:129 , ALA B:175 , VAL B:176 , GLY B:177 , LEU B:195 , LYS B:196 , THR B:239 , ARG B:344 , GLY B:382 , ASP B:383 , PRO B:391 , THR B:392 , ALA B:393 , GLN B:394 , ALA B:396 , TYR B:482 , MG B:608 , MG B:609 , MG B:610 , MG B:611 , HOH B:704 , HOH B:727 , HOH B:793 , HOH B:817BINDING SITE FOR RESIDUE FAD B 607
15BC6SOFTWAREALA B:175 , VAL B:176 , GLY B:177 , ILE B:381 , GLY B:382 , ASP B:383 , ASN B:384 , FAD B:607BINDING SITE FOR RESIDUE MG B 608
16BC7SOFTWAREGLY B:62 , GLY B:64 , ALA B:65 , ALA B:175 , FAD B:607BINDING SITE FOR RESIDUE MG B 609
17BC8SOFTWAREGLY B:62 , ARG B:85 , LEU B:89 , FAD B:607 , HOH B:727BINDING SITE FOR RESIDUE MG B 610
18BC9SOFTWAREGLY B:177 , ALA B:178 , LYS B:196 , ASP B:383 , FAD B:607BINDING SITE FOR RESIDUE MG B 611

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G6G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G6G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G6G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G6G)

(-) Exons   (0, 0)

(no "Exon" information available for 4G6G)

(-) Sequences/Alignments

Asymmetric/Biological 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:470
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee........eeeee..hhhhhhhhhhh.....eeeee....eee.hhhhhhh.....hhhh.eeehhhhhhh....eeeeeeeeeeeehhh.eeeeeeeeeeee...............eeee..eeee...eee......hhhhhhee..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhheeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee..........hhhhhhhhhhhhhhh..eee..eeeeee...eeeeeee.....eeeeeee..eeee...eeehhhhhhhhhhhhhhh.....ee............eee....ee.....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhh..........eeeee.....eeeeeee..eeeeeeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g6g A  36 GPTSFKTMKVIDPQHSDKPNVLILGSGWGAISFLKHIDTKKYNVSIISPRSYFLFTPLLPSAPVGTVDEKSIIEPIVNFALKKKGNVTYYEAEATSINPDRNTVTIKSLSAVSQLYQPENHLGLHQAEPAEIKYDYLISAVGAEPNTFGIPGVTDYGHFLKEIPNSLEIRRTFAANLEKANLLPKGDPERRRLLSIVVVGGGPTGVEAAGELQDYVHQDLRKFLPALAEEVQIHLVEALPIVLNMFEKKLSSYAQSHLENTSIKVHLRTAVAKVEEKQLLAKTKHEDGKITEETIPYGTLIWATGNKARPVITDLFKKIPEQNSSKRGLAVNDFLQVKGSNNIFAIGDNAFAGLPPTAQVAHQEAEYLAKNFDKMAQIPNFQKIDLLFEENNFKPFKYNDLGALAYLGSERAIATIRSGKRTFYTGGGLMTFYLWRILYLSMILSARSRLKVFFDWIKLAFFKRDFFKGL 513
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415 ||    433       443       453       463       473       483       493       503       513
                                                                                                                                                                                                                                                                                                                                                                                                                       417|                                                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                        426                                                                                       


Chain B from PDB  Type:PROTEIN  Length:463
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee........eeeee..hhhhhhhhhhh.....eeeeee...eee.hhhhhhh.....hhhh.eeehhhhhhh....eeeeeeeeeeeehhh.eeeeeeeeeeee...............eeee..eeee...eee......hhhhhhee..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhheeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee..........hhhhhhhhhhhhhhh..eee..eeeeee...eeeeeee.....eeeeeee..eeee...eeehhhhhhhhhhhhhhh.....ee............eee....ee.....hhhhhhhhhhhhhhhhhhhh.hhhhhhh.hhhhh..........eeeee.....eeeeeee..eeeeeeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g6g B  42 TMKVIDPQHSDKPNVLILGSGWGAISFLKHIDTKKYNVSIISPRSYFLFTPLLPSAPVGTVDEKSIIEPIVNFALKKKGNVTYYEAEATSINPDRNTVTIKSLSAVSQLYQPENHLGLHQAEPAEIKYDYLISAVGAEPNTFGIPGVTDYGHFLKEIPNSLEIRRTFAANLEKANLLPKGDPERRRLLSIVVVGGGPTGVEAAGELQDYVHQDLRKFLPALAEEVQIHLVEALPIVLNMFEKKLSSYAQSHLENTSIKVHLRTAVAKVEEKQLLAKTKHEDGKITEETIPYGTLIWATGNKARPVITDLFKKIPEQNSSKRGLAVNDFLQVKGSNNIFAIGDNAFAGLPPTAQVAHQEAEYLAKNFDKMAQIPNFQKNLLFEENNFKPFKYNDLGALAYLGSERAIATIRSGKRTFYTGGGLMTFYLWRILYLSMILSARSRLKVFFDWIKLAFFKRDFFKGL 513
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       430       440       450       460       470       480       490       500       510   
                                                                                                                                                                                                                                                                                                                                                                                                                   419|                                                                                    
                                                                                                                                                                                                                                                                                                                                                                                                                    429
   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 4G6G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G6G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G6G)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        NDI1_YEAST | P32340: 4g6h 4g73 4g74 4g9k 4gap 4gav

(-) Related Entries Specified in the PDB File

4g6h 4g73 4g74