Structure of PDB 5ud6 Chain D Binding Site BS02

Receptor Information

>5ud6 Chain D (length=299) Species: 280699 (Cyanidioschyzon merolae strain 10D) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

KHFFGRVITALVTPFKLTGVEVDYGVAESLAAHLAENGSDAIIVAGTTGE
SATLTWSEEYELFRVVKSAVAGTKCRVIAGAGSNSTEEAIEATKKSAKLG
LDGTLQVVPYYNKPPQQGIMAHFRAIANAAPDLPMMLYNIPGRTGINMTA
ETSIKLAEMCPNIVALKEASGNLEQFARIRRATSPDFALYSGDDALTLPL
LSLGGNGVVSVASHFIGPEIQRMIEHFVDLGNPEEAFRIHCRYMDLFEAL
FVMANPIPAKAALRLLGWPVGPTRLPLTDITASAEQQLRQAMIAAGLLS

Ligand information

Ligand ID

InChI

InChI=1S/Ca/q+2

InChIKey

BHPQYMZQTOCNFJ-UHFFFAOYSA-N

SMILES

Software	SMILES
CACTVS 3.341	[Ca++]
ACDLabs 10.04 OpenEye OEToolkits 1.5.0	[Ca+2]

Formula

Name

CALCIUM ION

PDB chain

5ud6 Chain D Residue 401 [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	5ud6 Crystal structure of DHDPS from Cyanidioschyzon merolae with lysine bound
Resolution	2.4 Å
Binding residue (original residue number in PDB)	A52 S58 E66 G87
Binding residue (residue number reindexed from 1)	A45 S51 E59 G80
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	T54 Y118 Y145 R150 K174 V216
Catalytic site (residue number reindexed from 1)	T47 Y111 Y138 R143 K167 V209
Enzyme Commision number	4.3.3.7: 4-hydroxy-tetrahydrodipicolinate synthase.

Gene Ontology

	Molecular Function
GO:0008840	4-hydroxy-tetrahydrodipicolinate synthase activity
GO:0016829	lyase activity

	Biological Process
GO:0009089	lysine biosynthetic process via diaminopimelate

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Molecular Function

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Biological Process

External links

PDB	RCSB:5ud6, PDBe:5ud6, PDBj:5ud6
PDBsum	5ud6
PubMed
UniProt	M1V4H9

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