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Receptor Information

>2jim Chain A (length=720) Species: 876 (Desulfovibrio desulfuricans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

RPEKWVKGVCRYCGTGCGVLVGVKDGKAVAIQGNPNNHNAGLLCLKGSLL
IPVLNSKERVTQPLVRRHKGGKLEPVSWDEALDLMASRFRSSIDMYGPNS
VAWYGSGQCLTEESYVANKIFKGGFGTNNVDGNPRLCMASAVGGYVTSFG
KDEPMGTYADIDQATCFFIIGSNTSEAHPVLFRRIARRKQVEPGVKIIVA
DPRRTNTSRIADMHVAFRPGTDLAFMHSMAWVIINEELDNPRFWQRYVNF
MDAEGKPSDFEGYKAFLENYRPEKVAEICRVPVEQIYGAARAFAESAATM
SLWCMGINQRVQGVFANNLIHNLHLITGQICRPGATSFSLTGQPNACGGV
RDGGALSHLLPAGRAIPNAKHRAEMEKLWGLPEGRIAPEPGYHTVALFEA
LGRGDVKCMIICETNPAHTLPNLNKVHKAMSHPESFIVCIEAFPDAVTLE
YADLVLPPAFWCERDGVYGCGERRYSLTEKAVDPPGQCRPTVNTLVEFAR
RAGVDPQLVNFRNAEDVWNEWRMVSKGTTYDFWGMTRERLRKESGLIWPC
PSEDHPGTSLRYVRGQDPCVPADHPDRFFFYGKPDGRAVIWMRPAKGAAE
EPDAEYPLYLTSMRVIDHWHTATMTGKVPELQKANPIAFVEINEEDAART
GIKHGDSVIVETRRDAMELPARVSDVCRPGLIAVPFFDPKKLVNKLFLDA
TDPVSREPEYKICAARVRKA

Ligand ID

MGD

InChI

InChI=1S/C20H26N10O13P2S2/c21-19-26-13-7(15(33)28-19)24-6-12(47)11(46)5(41-17(6)25-13)2-40-45(37,38)43-44(35,36)39-1-4-9(31)10(32)18(42-4)30-3-23-8-14(30)27-20(22)29-16(8)34/h3-6,9-10,17-18,24,31-32,46-47H,1-2H2,(H,35,36)(H,37,38)(H3,22,27,29,34)(H4,21,25,26,28,33)/t4-,5-,6+,9-,10-,17-,18-/m1/s1

InChIKey

VQAGYJCYOLHZDH-ILXWUORBSA-N

SMILES

Software	SMILES
CACTVS 3.341	NC1=NC2=C(N[CH]3[CH](N2)O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1
OpenEye OEToolkits 1.5.0	c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(=C(C5C(O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0	c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4C(=C([C@H]5[C@@H](O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
ACDLabs 10.04	O=C1C=2NC3C(S)=C(S)C(OC3NC=2N=C(N)N1)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c5N=C(N)NC4=O)C(O)C6O
CACTVS 3.341	NC1=NC2=C(N[C@@H]3[C@H](N2)O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1

Formula

C20 H26 N10 O13 P2 S2

Name

2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE;
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE

PDB chain

2jim Chain A Residue 812 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	2jim Periplasmic Nitrate Reductase Revisited: A Sulfur Atom Completes the Sixth Coordination of the Catalytic Molybdenum.
Resolution	2.45 Å
Binding residue (original residue number in PDB)	K49 G174 S175 N176 E179 A180 D204 P205 R206 D225 C307 M308 G309 R313 G345 Q346 M616 R617 V618 I619 W622 H623 K714
Binding residue (residue number reindexed from 1)	K46 G171 S172 N173 E176 A177 D201 P202 R203 D222 C304 M305 G306 R310 G342 Q343 M613 R614 V615 I616 W619 H620 K711
Annotation score	1

Catalytic site (original residue number in PDB)	K49 S109 C140 M141 A180 M308 T344 G345 Q346
Catalytic site (residue number reindexed from 1)	K46 S106 C137 M138 A177 M305 T341 G342 Q343
Enzyme Commision number	1.9.6.1: nitrate reductase (cytochrome).

	Molecular Function
GO:0005506	iron ion binding
GO:0008940	nitrate reductase activity
GO:0009055	electron transfer activity
GO:0016491	oxidoreductase activity
GO:0030151	molybdenum ion binding
GO:0043546	molybdopterin cofactor binding
GO:0046872	metal ion binding
GO:0050140	nitrate reductase (cytochrome) activity
GO:0051539	4 iron, 4 sulfur cluster binding

	Biological Process
GO:0006777	Mo-molybdopterin cofactor biosynthetic process
GO:0042128	nitrate assimilation

	Cellular Component
GO:0042597	periplasmic space

PDB	RCSB:2jim, PDBe:2jim, PDBj:2jim
PDBsum	2jim
PubMed	18327621
UniProt	P81186\|NAPA_DESDA Periplasmic nitrate reductase (Gene Name=napA)

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Structure of PDB 2jim Chain A Binding Site BS03