Structure of PDB 1f06 Chain B

Receptor sequence

>1f06B (length=320) Species: 1718 (Corynebacterium glutamicum)

MTNIRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRATLDTKTPVFDVA
DVDKHADDVDVLFLCMGSATDIPEQAPKFAQFACTVDTYDNHRDIPRHRQ
VMNEAATAAGNVALVSTGWDPGMFSINRVYAAAVLAEHQQHTFWGPGLSQ
GHSDALRRIPGVQKAVQYTLPSEDALEKARRGEAGDLTGKQTHKRQCFVV
ADAADHERIENDIRTMPDYFVGYEVEVNFIDEATFDSEHTGMPHGGHVIT
TGDTGGFNHTVEYILKLDRNPDFTASSQIAFGRAAHRMKQQGQSGAFTVL
EVAPYLLSPENLDDLIARDV

3D structure

• PDB: 1f06 The three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-pimelate.
• Chain: B
• Resolution: 2.1 Å

Enzymatic activity

• Enzyme Commision number: 1.4.1.16: diaminopimelate dehydrogenase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	NDP	B	G510 G512 N513 L514 S535 R536 R537 C565 S568 T588 D590 T617 G618 W619 Q650 G651 T774	G10 G12 N13 L14 S35 R36 R37 C65 S68 T88 D90 T117 G118 W119 Q150 G151 T274
BS02	2NP	B	D590 W619 W644 S649 Q650 G651 H652 T669 R695 H744 N770	D90 W119 W144 S149 Q150 G151 H152 T169 R195 H244 N270	MOAD: Ki=5uM

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity
• GO:0047850 diaminopimelate dehydrogenase activity

Biological Process

• GO:0009085 lysine biosynthetic process
• GO:0009089 lysine biosynthetic process via diaminopimelate
• GO:0019877 diaminopimelate biosynthetic process

External links

• PDB: RCSB:1f06, PDBe:1f06, PDBj:1f06
• PDBsum: 1f06
• PubMed: 11106178
• UniProt: P04964|DAPDH_CORGL Meso-diaminopimelate D-dehydrogenase (Gene Name=ddh)