Structure of PDB 2ekl Chain A Binding Site BS01

Receptor Information

>2ekl Chain A (length=312) Species: 111955 (Sulfurisphaera tokodaii)

AIYTVKALITDPIDEILIKTLREKGIQVDYMPEISKEELLNIIGNYDIIV
VRSRTKVTKDVIEKGKKLKIIARAGIGLDNIDTEEAEKRNIKVVYAPGAS
TDSAVELTIGLMIAAARKMYTSMALAKSGIFKKIEGLELAGKTIGIVGFG
RIGTKVGIIANAMGMKVLAYDILDIREKAEKINAKAVSLEELLKNSDVIS
LHVTVSKDAKPIIDYPQFELMKDNVIIVNTSRAVAVNGKALLDYIKKGKV
YAYATDVFWNEPPKEEWELELLKHERVIVTTHIGAQTKEAQKRVAEMTTQ
NLLNAMKELGMI

Ligand information

• Ligand ID: NAD
• InChI: InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: BAWFJGJZGIEFAR-NNYOXOHSSA-N
• SMILES:
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
• Formula: C21 H27 N7 O14 P2
• Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
• ChEMBL: CHEMBL1234613
• DrugBank: DB14128
• PDB chain: 2ekl Chain A Residue 1300

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ekl Structure of ST1218 protein from Sulfolobus tokodaii
• Resolution: 1.77 Å
• Binding residue (original residue number in PDB): I77 S101 G149 G151 R152 I153 Y171 D172 I173 L174 H203 V204 T205 I213 T231 S232 D257 G285
• Binding residue (residue number reindexed from 1): I76 S100 G148 G150 R151 I152 Y170 D171 I172 L173 H202 V203 T204 I212 T230 S231 D256 G284
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): S101 R233 D257 E262 H283
• Catalytic site (residue number reindexed from 1): S100 R232 D256 E261 H282
• Enzyme Commision number: 1.1.1.95: phosphoglycerate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0004617 phosphoglycerate dehydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0051287 NAD binding

External links

• PDB: RCSB:2ekl, PDBe:2ekl, PDBj:2ekl
• PDBsum: 2ekl
• UniProt: Q972A9