Structure of PDB 2vzu Chain B Binding Site BS01

Receptor Information

>2vzu Chain B (length=850) Species: 31958 (Amycolatopsis orientalis)

GNATPIPGYVIQSSAQVSDDSAVSKPGFPTSGWYPVSSRSTVYAGLLQNG
KYADPFYSTNMQNVPAAQFSVPWWYRTDLNVDDTSSRTYLDFSGVLSKAD
VWVNGTKVATKDQVNGAYTRHDLDITAQVHTGVNSVAFKVYPNDPNRDLS
MGWIDWAQTPPDQNMGIVRDVLVRRSGAVALRSAHVIQKLNSALDHADLT
VKADVRNDSANAVQTTVAGTVAGKPISQTVSLAAKERKTVTFPLVGLDRP
NVWWPAGMGGQHRYDLDLTASVGGTPSDAAKSKFGVRDVKATLNSSGGRQ
YSVNGKPLLIRGGGYTPDLFLRWNETAAADKLKYVLNLGLNTVRLEGHIE
PDEFFDIADDLGVLTMPGWECCDKWEGQVNGEEKGEPWVESDYPIAKASM
FSEAERLRDHPSVISFHIGSAFAPDRRIEQGYLDAMKAADFLLPVIPAAS
ARPSPITGASGMKMNGPYDYVPPVYWYDKSQKDRGGAWSFNSETSAGVDI
PTMDTLKRMMSASELDTMWKNPSAKQYHRSSSDTFGNLKLFGDALTKRYG
ASANLNDFVRKAQLSQYENVRAEFESHSRNYTDSTNPSTGLIYWMLNSPW
TSLHWQLFDAYMDQNGAYYGAKKANEPLHIQYSHDNRSVVVINQTSNAVS
GLTATTKLYNLDGTEKYSNTKTGLSVGALGAKATAVTVPAVSGLSTTYLA
KNVLTDSSGKEVSRNVYWLSTKADTLNWGGSDWYYTPQSAFADLSGLNNL
GQSAVGATANSVAGADGTTTTTVTLKNTSGGRLPAFYVDSKVVDSAGKPV
LPVEWNANAVSLWPGETTTLTAKYRTADLKGSKPSVRISGWNTGTQTVPA

Ligand information

• Ligand ID: PNJ
• InChI: InChI=1S/C12H16N2O7/c13-9-11(17)10(16)8(5-15)21-12(9)20-7-3-1-6(2-4-7)14(18)19/h1-4,8-12,15-17H,5,13H2/t8-,9-,10-,11-,12-/m1/s1
• InChIKey: ZRNBGANFPXCMFT-LZQZFOIKSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1cc(ccc1[N+](=O)[O-])O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)N
  OpenEye OEToolkits 2.0.7: c1cc(ccc1[N+](=O)[O-])OC2C(C(C(C(O2)CO)O)O)N
  CACTVS 3.385: N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1Oc2ccc(cc2)[N+]([O-])=O
  CACTVS 3.385: N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]1Oc2ccc(cc2)[N+]([O-])=O
• Formula: C12 H16 N2 O7
• Name: 4-nitrophenyl 2-amino-2-deoxy-beta-D-glucopyranoside;
  PNP-BETA-D-GLUCOSAMINE;
  4-nitrophenyl 2-amino-2-deoxy-beta-D-glucoside;
  4-nitrophenyl 2-amino-2-deoxy-D-glucoside;
  4-nitrophenyl 2-amino-2-deoxy-glucoside
• PDB chain: 2vzu Chain B Residue 1904

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2vzu The Structural Basis of Substrate Recognition in an Exo-Beta-D-Glucosaminidase Involved in Chitosan Hydrolysis.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): I202 D203 W204 E394 C419 M512 Y516 E541 W642 W653 W781
• Binding residue (residue number reindexed from 1): I154 D155 W156 E346 C371 M464 Y468 E493 W594 W605 W733
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.2.1.165: exo-1,4-beta-D-glucosaminidase.

Gene Ontology

Molecular Function

• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0030246 carbohydrate binding

Biological Process

• GO:0005975 carbohydrate metabolic process

External links

• PDB: RCSB:2vzu, PDBe:2vzu, PDBj:2vzu
• PDBsum: 2vzu
• PubMed: 18976664
• UniProt: Q56F26|EBDG_AMYOR Exo-beta-D-glucosaminidase (Gene Name=csxA)