Structure of PDB 5yz2 Chain B Binding Site BS01

Receptor Information

>5yz2 Chain B (length=136) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ELALQRVRDIMIPRSQMITLKRNQTLDECLDVIIESAHSRFPVISEDKDH
IEGILMAKDLLPFMRSDAEAFSMDKVLRQAVVVPESKRVDRMLKEFRSQR
YHMAIVIDEFGGVSGLVTIEDILELIVGEIEKGQFL

Ligand information

Ligand ID

AMP

InChI

InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1

InChIKey

UDMBCSSLTHHNCD-KQYNXXCUSA-N

SMILES

Software	SMILES
CACTVS 3.370	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6	c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01	O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N

Formula

C10 H14 N5 O7 P

Name

ADENOSINE MONOPHOSPHATE

PDB chain

5yz2 Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5yz2 The C2'- and C3'-endo equilibrium for AMP molecules bound in the cystathionine-beta-synthase domain.
Resolution	1.75 Å
Binding residue (original residue number in PDB)	I74 M79 I80 H100 S101 T180 D183
Binding residue (residue number reindexed from 1)	I12 M17 I18 H38 S39 T118 D121
Annotation score	4
Binding affinity	MOAD: Kd=11.3uM PDBbind-CN: -logKd/Ki=4.95,Kd=11.3uM

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:5yz2, PDBe:5yz2, PDBj:5yz2
PDBsum	5yz2
PubMed	29453981
UniProt	P0AE78\|CORC_ECOLI Magnesium and cobalt efflux protein CorC (Gene Name=corC)

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