4DQL - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE FAD BINDING DOMAIN OF CYTOCHROME P450 BM3 IN COMPLEX WITH NADP+

Authors :   M. G. Joyce, D. Leys

Date :   16 Feb 12 (Deposition) - 07 Mar 12 (Release) - 06 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (1x),B (1x)

Keywords :   Rossmann Fold, Redox, Fad And Nadp+ Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. G. Joyce, I. S. Ekanem, O. Roitel, A. J. Dunford, R. Neeli, H. M. Girvan, G. J. Baker, R. A. Curtis, A. W. Munro, D. Leys
The Crystal Structure Of The Fad/Nadph-Binding Domain Of Flavocytochrome P450 Bm3.
Febs J. V. 279 1694 2012
PubMed-ID: 22356131 | Reference-DOI: 10.1111/J.1742-4658.2012.08544.X

Molecule 1 - BIFUNCTIONAL P-450/NADPH-P450 REDUCTASE
	Chains	:	A, B
	EC Number	:	1.14.14.1, 1.6.2.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	CYTOCHROME P450 BM3,UNP RESIDUES 657-1049
	Gene	:	CYP102A1, CYP102
	Organism Scientific	:	BACILLUS MEGATERIUM
	Organism Taxid	:	1404
	Synonym	:	CYTOCHROME P450(BM-3), CYTOCHROME P450BM-3, CYTOCHROME P450 102, NADPH--CYTOCHROME P450 REDUCTASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 10)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4	PG4	3	Ligand/Ion	TETRAETHYLENE GLYCOL
5	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (5, 5)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 5)

No.	Name	Count	Type	Full Name
1	1PE	-1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4	PG4	2	Ligand/Ion	TETRAETHYLENE GLYCOL
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (5, 5)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
5	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:700 , GLN A:757 , ARG A:798 , ARG A:828 , TYR A:829 , TYR A:830 , SER A:831 , THR A:846 , VAL A:847 , SER A:848 , GLU A:853 , ALA A:854 , TRP A:855 , TYR A:861 , GLY A:863 , ILE A:864 , ALA A:865 , SER A:866 , THR A:906 , TRP A:1047 , GLY A:1049 , HOH A:1206 , HOH A:1210 , HOH A:1213 , HOH A:1237 , HOH A:1242 , HOH A:1277 , HOH A:1320 , HOH A:1443 , HOH A:1474	BINDING SITE FOR RESIDUE FAD A 1101
02	AC2	SOFTWARE	ARG A:680 , SER A:848 , VAL A:850 , GLY A:905 , THR A:906 , CYS A:937 , ARG A:938 , SER A:966 , ARG A:967 , TYR A:975 , GLN A:977 , MET A:1006 , HOH A:1212 , HOH A:1220 , HOH A:1234 , HOH A:1244 , HOH A:1280 , HOH A:1375 , HOH A:1412 , HOH A:1416 , HOH A:1418 , HOH A:1524 , HOH A:1526 , HOH A:1555	BINDING SITE FOR RESIDUE NAP A 1102
03	AC3	SOFTWARE	PRO A:892 , LYS A:893 , HIS A:996 , HOH A:1271 , HOH A:1289 , HOH A:1398 , HIS B:660	BINDING SITE FOR RESIDUE SO4 A 1103
04	AC4	SOFTWARE	ASP A:992 , TRP A:1032 , GLN A:1035 , LEU A:1036 , LYS A:1039 , ARG A:1041 , HOH A:1219 , HOH B:1458	BINDING SITE FOR RESIDUE 1PE A 1104
05	AC5	SOFTWARE	LYS A:671 , GLU A:672 , LEU A:673 , TYR A:946 , GLU A:949 , HOH A:1558	BINDING SITE FOR RESIDUE PG4 A 1105
06	AC6	SOFTWARE	GLN A:1035 , GLU A:1038 , HIS B:700 , GLN B:757 , ARG B:798 , ARG B:828 , TYR B:829 , TYR B:830 , SER B:831 , THR B:846 , VAL B:847 , SER B:848 , VAL B:850 , GLU B:853 , ALA B:854 , TRP B:855 , TYR B:861 , GLY B:863 , ILE B:864 , ALA B:865 , SER B:866 , TRP B:1047 , GLY B:1049 , HOH B:1203 , HOH B:1219 , HOH B:1223 , HOH B:1236 , HOH B:1279 , HOH B:1352 , HOH B:1374 , HOH B:1410 , HOH B:1417 , HOH B:1466	BINDING SITE FOR RESIDUE FAD B 1101
07	AC7	SOFTWARE	ARG B:680 , GLY B:905 , THR B:906 , CYS B:937 , ARG B:938 , SER B:966 , ARG B:967 , LYS B:973 , TYR B:975 , GLN B:977 , GLN B:1005 , MET B:1006 , HOH B:1237 , HOH B:1238 , HOH B:1246 , HOH B:1257 , HOH B:1300 , HOH B:1451	BINDING SITE FOR RESIDUE NAP B 1102
08	AC8	SOFTWARE	ARG B:762 , ARG B:766	BINDING SITE FOR RESIDUE SO4 B 1103
09	AC9	SOFTWARE	LYS B:671 , LEU B:673 , ARG B:912 , TYR B:946 , GLU B:949 , HOH B:1440	BINDING SITE FOR RESIDUE PG4 B 1104
10	BC1	SOFTWARE	TYR B:858 , GLY B:859 , GLU B:860 , HOH B:1431 , HOH B:1528	BINDING SITE FOR RESIDUE PG4 B 1105

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

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

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FAD_FR	PS51384	Ferredoxin reductase-type FAD binding domain profile.	CPXB_BACMB	660-892	1	B:660-892

Biological Unit 1 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FAD_FR	PS51384	Ferredoxin reductase-type FAD binding domain profile.	CPXB_BACMB	660-892	0	-

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FAD_FR	PS51384	Ferredoxin reductase-type FAD binding domain profile.	CPXB_BACMB	660-892	1	B:660-892

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FAD_FR	PS51384	Ferredoxin reductase-type FAD binding domain profile.	CPXB_BACMB	660-892	1	B:660-892

(no "Exon" information available for 4DQL)

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:378
 aligned with CPXB_BACMB | P14779 from UniProtKB/Swiss-Prot  Length:1049

    Alignment length:389
                                   670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040         
          CPXB_BACMB    661 GAFSTNVVASKELQQPGSARSTRHLEIELPKEASYQEGDHLGVIPRNYEGIVNRVTARFGLDASQQIRLEAEEEKLAHLPLAKTVSVEELLQYVELQDPVTRTQLRAMAAKTVCPPHKVELEALLEKQAYKEQVLAKRLTMLELLEKYPACEMKFSEFIALLPSIRPRYYSISSSPRVDEKQASITVSVVSGEAWSGYGEYKGIASNYLAELQEGDTITCFISTPQSEFTLPKDPETPLIMVGPGTGVAPFRGFVQARKQLKEQGQSLGEAHLYFGCRSPHEDYLYQEELENAQSEGIITLHTAFSRMPNQPKTYVQHVMEQDGKKLIELLDQGAHFYICGDGSQMAPAVEATLMKSYADVHQVSEADARLWLQQLEEKGRYAKDVWAG 1049
               SCOP domains d4dqla1 A:661-887 automated matches                                                                                                                                                                                                d4dqla2 A:888-1049 automated matches                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.........eeeeeee...........eeee....hhhhhhhhhhhhh.....ee...-----------...eehhhhh.........hhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhh.....hhhhhhhh......eeee..........eeeeeee..eee......eeehhhhhhhhhh....eeeeeee...............eeee.hhhhhhhhhhhhhhhhhhhhh......eeeeeee........hhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE FAD_FR  PDB: - UniProt: 660-892                                                                                                                                                                                                         ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4dql A  661 GAFSTNVVASKELQQPGSARSTRHLEIELPKEASYQEGDHLGVIPRNYEGIVNRVTARFGLDASQQIRLE-----------AKTVSVEELLQYVELQDPVTRTQLRAMAAKTVCPPHKVELEALLEKQAYKEQVLAKRLTMLELLEKYPACEMKFSEFIALLPSIRPRYYSISSSPRVDEKQASITVSVVSGEAWSGYGEYKGIASNYLAELQEGDTITCFISTPQSEFTLPKDPETPLIMVGPGTGVAPFRGFVQARKQLKEQGQSLGEAHLYFGCRSPHEDYLYQEELENAQSEGIITLHTAFSRMPNQPKTYVQHVMEQDGKKLIELLDQGAHFYICGDGSQMAPAVEATLMKSYADVHQVSEADARLWLQQLEEKGRYAKDVWAG 1049
                                   670       680       690       700       710       720       730         - |     750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040         
                                                                                               730         742

Chain B from PDB  Type:PROTEIN  Length:379
 aligned with CPXB_BACMB | P14779 from UniProtKB/Swiss-Prot  Length:1049

    Alignment length:392
                                   667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047  
          CPXB_BACMB    658 KMHGAFSTNVVASKELQQPGSARSTRHLEIELPKEASYQEGDHLGVIPRNYEGIVNRVTARFGLDASQQIRLEAEEEKLAHLPLAKTVSVEELLQYVELQDPVTRTQLRAMAAKTVCPPHKVELEALLEKQAYKEQVLAKRLTMLELLEKYPACEMKFSEFIALLPSIRPRYYSISSSPRVDEKQASITVSVVSGEAWSGYGEYKGIASNYLAELQEGDTITCFISTPQSEFTLPKDPETPLIMVGPGTGVAPFRGFVQARKQLKEQGQSLGEAHLYFGCRSPHEDYLYQEELENAQSEGIITLHTAFSRMPNQPKTYVQHVMEQDGKKLIELLDQGAHFYICGDGSQMAPAVEATLMKSYADVHQVSEADARLWLQQLEEKGRYAKDVWAG 1049
               SCOP domains d4dqlb1 B:658-887 automated matches                                                                                                                                                                                                   d4dqlb2 B:888-1049 automated matches                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhheeeeeeeeee.........eeeeeee...........eeee....hhhhhhhhhhhhh.....ee..-------------..eehhhhh.........hhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhh.....hhhhhhhh......eeee..........eeeeeee..eee......eeehhhhhhhhhh....eeeeeee...............eeee.hhhhhhhhhhhhhhhhhhhhh......eeeeeee........hhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FAD_FR  PDB: B:660-892 UniProt: 660-892                                                                                                                                                                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4dql B  658 KMHGAFSTNVVASKELQQPGSARSTRHLEIELPKEASYQEGDHLGVIPRNYEGIVNRVTARFGLDASQQIRL-------------KTVSVEELLQYVELQDPVTRTQLRAMAAKTVCPPHKVELEALLEKQAYKEQVLAKRLTMLELLEKYPACEMKFSEFIALLPSIRPRYYSISSSPRVDEKQASITVSVVSGEAWSGYGEYKGIASNYLAELQEGDTITCFISTPQSEFTLPKDPETPLIMVGPGTGVAPFRGFVQARKQLKEQGQSLGEAHLYFGCRSPHEDYLYQEELENAQSEGIITLHTAFSRMPNQPKTYVQHVMEQDGKKLIELLDQGAHFYICGDGSQMAPAVEATLMKSYADVHQVSEADARLWLQQLEEKGRYAKDVWAG 1049
                                   667       677       687       697       707       717       727 |       -     | 747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047  
                                                                                                 729           743

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 '\|'

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (CPXB_BACMB | P14779)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0003958	NADPH-hemoprotein reductase activity	Catalysis of the reaction: NADPH + H+ + n oxidized hemoprotein = NADP+ + n reduced hemoprotein.
	GO:0070330	aromatase activity	Catalysis of the reduction of an aliphatic ring to yield an aromatic ring.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
	GO:0016712	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from reduced flavin or flavoprotein and one other donor, and one atom of oxygen is incorporated into one donor.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Cis Peptide Bonds
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	4dql
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4dqk	THE SAME PROTEIN WITHOUT NADP+ BOUND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (2, 4)

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Gene Ontology (15, 15)

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