Structure of PDB 1z7e Chain D Binding Site BS01

Receptor Information

>1z7e Chain D (length=644) Species: 562 (Escherichia coli)

MKTVVFAYHDMGCLGIEALLAAGYEISAIFTHTDGSVARLAAERGIPVYA
PDNVNHPLWVERIAQLSPDVIFSFYYRHLIYDEILQLAPAGAFNLHGSLL
PKYRGRAPLNWVLVNGETETGVTLHRMVKRADAGAIVAQLRIAIAPDDIA
ITLHHKLCHAARQLLEQTLPAIKHGNILEIAQRENEATCFGRRTPDDSFL
EWHKPASVLHNMVRAVADPWPGAFSYVGNQKFTVWSSRVHPHASKAQPGS
VISVAPLLIACGDGALEIVTGQAGDGITMQGSQLAQTLGLVQGSRLNSQP
RRRTRVLILGVNGFIGNHLTERLLREDHYEVYGLDIGSDAISRFLNHPHF
HFVEGDISIHSEWIEYHVKKCDVVLPLVAIATPIEYTRNPLRVFELDFEE
NLRIIRYCVKYRKRIIFPSTSEVYGMCSDKYFDEDHSNLIVGPVNKPRWI
YSVSKQLLDRVIWAYGEKEGLQFTLFRPFNWMGPRLDNLNAARIGSSRAI
TQLILNLVEGSPIKLIDGGKQKRCFTDIRDGIEALYRIIENAGNRCDGEI
INIGNPENEASIEELGEMLLASFEKHPLRHHFPPFAGFRVVESSSYYGKG
YQDVEHRKPSIRNAHRCLDWEPKIDMQETIDETLDFFLRTVDLT

Ligand information

• Ligand ID: ATP
• InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: ZKHQWZAMYRWXGA-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C10 H16 N5 O13 P3
• Name: ADENOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL14249
• DrugBank: DB00171
• ZINC: ZINC000004261765
• PDB chain: 1z7e Chain D Residue 1004

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1z7e Structure and Mechanism of ArnA: Conformational Change Implies Ordered Dehydrogenase Mechanism in Key Enzyme for Polymyxin Resistance
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): G325 F326 I327 D347 I348 D368 I369 V390 R510
• Binding residue (residue number reindexed from 1): G313 F314 I315 D335 I336 D356 I357 V378 R498
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): H104 D140
• Catalytic site (residue number reindexed from 1): H96 D132
• Enzyme Commision number: 1.1.1.305: UDP-glucuronic acid oxidase (UDP-4-keto-hexauronic acid decarboxylating).
  2.1.2.13: UDP-4-amino-4-deoxy-L-arabinose formyltransferase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0005515 protein binding
• GO:0016491 oxidoreductase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0016740 transferase activity
• GO:0016742 hydroxymethyl-, formyl- and related transferase activity
• GO:0016831 carboxy-lyase activity
• GO:0042802 identical protein binding
• GO:0048040 UDP-glucuronate decarboxylase activity
• GO:0070403 NAD+ binding
• GO:0099618 UDP-glucuronic acid dehydrogenase activity
• GO:0099619 UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity

Biological Process

• GO:0009058 biosynthetic process
• GO:0009103 lipopolysaccharide biosynthetic process
• GO:0009245 lipid A biosynthetic process
• GO:0033320 UDP-D-xylose biosynthetic process
• GO:0046493 lipid A metabolic process
• GO:0046677 response to antibiotic
• GO:2001315 UDP-4-deoxy-4-formamido-beta-L-arabinopyranose biosynthetic process

Cellular Component

• GO:0032991 protein-containing complex

External links

• PDB: RCSB:1z7e, PDBe:1z7e, PDBj:1z7e
• PDBsum: 1z7e
• PubMed: 15939024
• UniProt: P77398|ARNA_ECOLI Bifunctional polymyxin resistance protein ArnA (Gene Name=arnA)