Structure of PDB 1z7e Chain D Binding Site BS02

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: UGA
• InChI: InChI=1S/C15H22N2O18P2/c18-5-1-2-17(15(26)16-5)12-9(22)6(19)4(32-12)3-31-36(27,28)35-37(29,30)34-14-10(23)7(20)8(21)11(33-14)13(24)25/h1-2,4,6-12,14,19-23H,3H2,(H,24,25)(H,27,28)(H,29,30)(H,16,18,26)/t4-,6-,7+,8+,9-,10-,11+,12-,14-/m1/s1
• InChIKey: HDYANYHVCAPMJV-LXQIFKJMSA-N
• SMILES:
  ACDLabs 10.04: O=C(O)C3OC(OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O)C(O)C(O)C3O
  CACTVS 3.341: O[CH]1[CH](O)[CH](O[CH]([CH]1O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)C(=O)O)O)O)O)O)O
  CACTVS 3.341: O[C@@H]1[C@@H](O)[C@H](O[C@@H]([C@H]1O)C(O)=O)O[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)C(=O)O)O)O)O)O)O
• Formula: C15 H22 N2 O18 P2
• Name: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID;
  UDP-GLUCURONIC ACID
• ChEMBL: CHEMBL228057
• DrugBank: DB03041
• ZINC: ZINC000008215691
• PDB chain: 1z7e Chain D Residue 1104

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): A393 P395 Y398 E434 Y463 F491 N492 R510 A511 K526 L527 I528 R535 I574 Y609 Y613 R619
• Binding residue (residue number reindexed from 1): A381 P383 Y386 E422 Y451 F479 N480 R498 A499 K514 L515 I516 R523 I562 Y597 Y601 R607
• Annotation score: 4

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)