Structure of PDB 3ml1 Chain A Binding Site BS03

Receptor Information

>3ml1 Chain A (length=799) Species: 381666 (Cupriavidus necator H16)

VTDSEVTKLKWSKAPCRFCGTGCGVTVAVKDNKVVATQGDPQAEVNKGLN
CVKGYFLSKIMYGQDRLTRPLMRMKNGKYDKNGDFAPVTWDQAFDEMERQ
FKRVLKEKGPTAVGMFGSGQWTVWEGYAAAKLYKAGFRSNNIDPNARHCM
ASAAAGFMRTFGMDEPMGCYDDFEAADAFVLWGSNMAEMHPILWTRVTDR
RLSHPKTRVVVLSTFTHRCFDLADIGIIFKPQTDLAMLNYIANYIIRNNK
VNKDFVNKHTVFKEGVTDIGYGLRPDHPLQKAAKNASDPGAAKVITFDEF
AKFVSKYDADYVSKLSAVPKAKLDQLAELYADPNIKVMSLWTMGFNQHTR
GTWANNMVYNLHLLTGKIATPGNSPFSLTGQPSACGTAREVGTFSHRLPA
DMVVTNPKHREEAERIWKLPPGTIPDKPGYDAVLQNRMLKDGKLNAYWVQ
VNNNMQAAANLMEEGLPGYRNPANFIVVSDAYPTVTALAADLVLPSAMWV
EKEGAYGNAERRTQFWHQLVDAPGEARSDLWQLVEFAKRFKVEEVWPPEL
IAKKPEYKGKTLYDVLYRNGQVDKFPLKDVNAEYHNAEAKAFGFYLQKGL
FEEYATFGRGHGHDLAPFDAYHEARGLRWPVVNGKETRWRYREGSDPYVK
AGTGFQFYGNPDGKAVIFALPYEPPAESPDKEYPYWLVTGRVLEHWHSGS
MTRRVPELYRSFPNAVVFMHPEDAKALGLRRGVEVEVVSRRGRMRSRIET
RGRDAPPRGLVFVPWFDASQLINKVTLDATCPISLQTDFKKCAVKIVKV

Ligand information

• 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:
  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
• ZINC: ZINC000195757106
• PDB chain: 3ml1 Chain A Residue 1804

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3ml1 The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): K56 W185 G186 N188 M192 S216 T217 F218 H220 F232 D237 T345 M346 G347 F348 G383 Q384 G693 R694 L696 H698 W699 H700 K793
• Binding residue (residue number reindexed from 1): K53 W182 G183 N185 M189 S213 T214 F215 H217 F229 D234 T342 M343 G344 F345 G380 Q381 G690 R691 L693 H695 W696 H697 K790
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): N53 C54 K56 G122 W124 C152 M153 M346 T382 G383 Q384
• Catalytic site (residue number reindexed from 1): N50 C51 K53 G119 W121 C149 M150 M343 T379 G380 Q381
• Enzyme Commision number: 1.9.6.1: nitrate reductase (cytochrome).

Gene Ontology

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
• GO:0045333 cellular respiration

Cellular Component

• GO:0042597 periplasmic space
• GO:1990204 oxidoreductase complex

External links

• PDB: RCSB:3ml1, PDBe:3ml1, PDBj:3ml1
• PDBsum: 3ml1
• PubMed: 21419779
• UniProt: P39185|NAPA_CUPNH Periplasmic nitrate reductase (Gene Name=napA)