4G6H - JenaLib

Title :   CRYSTAL STRUCTURE OF NDH WITH NADH

Authors :   W. Li, Y. Feng, J. Ge, M. Yang

Date :   19 Jul 12 (Deposition) - 24 Oct 12 (Release) - 06 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.26

Chains :   Asym./Biol. Unit : A,B

Keywords :   Rossmann Fold, Electron Transfer, Fad, Nadh, 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

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 10)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	MG	6	Ligand/Ion	MAGNESIUM ION
3	NAI	2	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY 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 , NAI A:602 , HOH A:701 , HOH A:706 , HOH A:707 , HOH A:709 , HOH A:713 , HOH A:730 , HOH A:731 , HOH A:733 , HOH A:740 , HOH A:768 , HOH A:824	BINDING SITE FOR RESIDUE FAD A 601
02	AC2	SOFTWARE	VAL A:234 , GLY A:235 , GLY A:237 , PRO A:238 , THR A:239 , GLU A:242 , GLU A:272 , ALA A:273 , LEU A:274 , THR A:304 , ALA A:305 , VAL A:306 , ALA A:338 , THR A:339 , GLY A:340 , ASN A:341 , PRO A:391 , THR A:392 , FAD A:601 , HOH A:701 , HOH A:723 , HOH A:761 , HOH A:770 , HOH A:774 , HOH A:809 , HOH A:815 , HOH A:827 , HOH A:863 , HOH A:921 , HOH A:956	BINDING SITE FOR RESIDUE NAI A 602
03	AC3	SOFTWARE	THR A:189 , GLY A:192 , HOH A:757 , HOH A:765	BINDING SITE FOR RESIDUE MG A 603
04	AC4	SOFTWARE	VAL A:266 , SER A:297 , HOH A:714 , HOH A:736 , HOH A:856	BINDING SITE FOR RESIDUE MG A 604
05	AC5	SOFTWARE	PRO A:48 , GLN A:49 , SER A:51 , LYS A:53 , ASN A:55	BINDING SITE FOR RESIDUE MG A 605
06	AC6	SOFTWARE	GLU B:203	BINDING SITE FOR RESIDUE MG B 601
07	AC7	SOFTWARE	GLY B:333 , HOH B:727 , HOH B:728 , HOH B:818	BINDING SITE FOR RESIDUE MG B 602
08	AC8	SOFTWARE	PRO B:134 , ASN B:137 , TYR B:169 , ASN B:377 , ILE B:378 , HOH B:908	BINDING SITE FOR RESIDUE MG B 603
09	AC9	SOFTWARE	VAL B:234 , GLY B:235 , PRO B:238 , THR B:239 , GLU B:242 , VAL B:271 , GLU B:272 , ALA B:273 , LEU B:274 , THR B:304 , ALA B:305 , VAL B:306 , THR B:339 , GLY B:340 , ASN B:341 , PRO B:391 , THR B:392 , FAD B:605 , HOH B:701 , HOH B:704 , HOH B:751 , HOH B:777 , HOH B:794 , HOH B:817 , HOH B:831 , HOH B:868 , HOH B:877 , HOH B:888	BINDING SITE FOR RESIDUE NAI B 604
10	BC1	SOFTWARE	GLY 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 , 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 , NAI B:604 , HOH B:701 , HOH B:703 , HOH B:720 , HOH B:726 , HOH B:730 , HOH B:735 , HOH B:738 , HOH B:741 , HOH B:784 , HOH B:801	BINDING SITE FOR RESIDUE FAD B 605

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:472
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee........eeeee..hhhhhhhhhhh.....eeeeee...eee.hhhhhhh.....hhhh.eeehhhhhh.....eeeeeeeeeeeehhh.eeeeeeeeeeee...............eeee..eeee....ee......hhhhhhee..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhheeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee..........hhhhhhhhhhhhhhh..eee..eeeeee...eeeeeee.....eeeeeee..eeee...ee.hhhhhhhhhhhhhhh.....ee............eee....ee.....hhhhhhhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhh..........eeeee.....eeeeeee..eeeeeeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g6h A  42 TMKVIDPQHSDKPNVLILGSGWGAISFLKHIDTKKYNVSIISPRSYFLFTPLLPSAPVGTVDEKSIIEPIVNFALKKKGNVTYYEAEATSINPDRNTVTIKSLSAVSQLYQPENHLGLHQAEPAEIKYDYLISAVGAEPNTFGIPGVTDYGHFLKEIPNSLEIRRTFAANLEKANLLPKGDPERRRLLSIVVVGGGPTGVEAAGELQDYVHQDLRKFLPALAEEVQIHLVEALPIVLNMFEKKLSSYAQSHLENTSIKVHLRTAVAKVEEKQLLAKTKHEDGKITEETIPYGTLIWATGNKARPVITDLFKKIPEQNSSKRGLAVNDFLQVKGSNNIFAIGDNAFAGLPPTAQVAHQEAEYLAKNFDKMAQIPNFQKNLSSRKDKIDLLFEENNFKPFKYNDLGALAYLGSERAIATIRSGKRTFYTGGGLMTFYLWRILYLSMILSARSRLKVFFDWIKLAFFKRDFFKGL 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       421       431       441       451       461       471       481       491       501       511

Chain B from PDB  Type:PROTEIN  Length:472
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee........eeeee..hhhhhhhhhhh.....eeeeee...eee.hhhhhhh.....hhhh.eeehhhhhh.....eeeeeeeeeeeehhh.eeeeeeeeeeeee..............eeee..eeee....ee......hhhhhhee..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhheeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee..........hhhhhhhhhhhhhhh..eee..eeeeee...eeeeeee.....eeeeeee..eeee...ee.hhhhhhhhhhhhhhh...................eee.hhhh......hhhhhhhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhh..........eeeee.....eeeeeee..eeeeeeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g6h B  42 TMKVIDPQHSDKPNVLILGSGWGAISFLKHIDTKKYNVSIISPRSYFLFTPLLPSAPVGTVDEKSIIEPIVNFALKKKGNVTYYEAEATSINPDRNTVTIKSLSAVSQLYQPENHLGLHQAEPAEIKYDYLISAVGAEPNTFGIPGVTDYGHFLKEIPNSLEIRRTFAANLEKANLLPKGDPERRRLLSIVVVGGGPTGVEAAGELQDYVHQDLRKFLPALAEEVQIHLVEALPIVLNMFEKKLSSYAQSHLENTSIKVHLRTAVAKVEEKQLLAKTKHEDGKITEETIPYGTLIWATGNKARPVITDLFKKIPEQNSSKRGLAVNDFLQVKGSNNIFAIGDNAFAGLPPTAQVAHQEAEYLAKNFDKMAQIPNFQKNLSSRKDKIDLLFEENNFKPFKYNDLGALAYLGSERAIATIRSGKRTFYTGGGLMTFYLWRILYLSMILSARSRLKVFFDWIKLAFFKRDFFKGL 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       421       431       441       451       461       471       481       491       501       511

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

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