Structure of PDB 6vvh Chain DDD Binding Site BS01

Receptor Information

>6vvh Chain DDD (length=312) Species: 3702 (Arabidopsis thaliana)

DKNRTNTDDIRSLRVITAIKTPYLPDGRFDLQAYDDLVNTQIENGAEGVI
VGGTTGEGQLMSWDEHIMLIGHTVNCFGGRIKVIGNTGSNSTREAIHATE
QGFAMGMHGALHINPYYGKTSIEGMNAHFQTVLHMGPTIIYNVPGRTCQD
IPPQVIFKLSQNPNMAGVKECVGNNRVEEYTEKGIVVWSGNDDQCHDSRW
DHGATGVISVTSNLVPGLMRKLMFEGRNSALNAKLLPLMDWLFQEPNPIG
VNTALAQLGVARPVFRLPYVPLPLSKRIEFVKLVKEIGREHFVGDRDVQV
LDDDDFILIGRY

Ligand information

• Ligand ID: LYS
• InChI: InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1/t5-/m0/s1
• InChIKey: KDXKERNSBIXSRK-YFKPBYRVSA-O
• SMILES:
  CACTVS 3.341: N[CH](CCCC[NH3+])C(O)=O
  ACDLabs 10.04: O=C(O)C(N)CCCC[NH3+]
  OpenEye OEToolkits 1.5.0: C(CC[NH3+])C[C@@H](C(=O)O)N
  CACTVS 3.341: N[C@@H](CCCC[NH3+])C(O)=O
  OpenEye OEToolkits 1.5.0: C(CC[NH3+])CC(C(=O)O)N
• Formula: C6 H15 N2 O2
• Name: LYSINE
• PDB chain: 6vvh Chain CCC Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vvh Differential lysine-mediated allosteric regulation of plant dihydrodipicolinate synthase isoforms.
• Resolution: 1.792 Å
• Binding residue (original residue number in PDB): N143 E147
• Binding residue (residue number reindexed from 1): N90 E94
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): T107 Y170 Y194 R199 K222 I261
• Catalytic site (residue number reindexed from 1): T54 Y117 Y141 R146 K169 I208
• 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

External links

• PDB: RCSB:6vvh, PDBe:6vvh, PDBj:6vvh
• PDBsum: 6vvh
• PubMed: 33586321
• UniProt: Q9LZX6|DAPA1_ARATH 4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic (Gene Name=DHDPS1)