Structure of PDB 1ndo Chain A

Receptor sequence

>1ndoA (length=447) Species: 303 (Pseudomonas putida)

MNYNNKILVSESGLSQKHLIHGDEELFQHELKTIFARNWLFLTHDSLIPA
PGDYVTAKMGIDEVIVSRQNDGSIRAFLNVCRHRGKTLVSVEAGNAKGFV
CSYHGWGFGSNGELQSVPFEKDLYGESLNKKCLGLKEVARVESFHGFIYG
CFDQEAPPLMDYLGDAAWYLEPMFKHSGGLELVGPPGKVVIKANWKAPAE
NFVGDAYHVGWTHASSLRSGESIFSSLAGNAALPPEGAGLQMTSKYGSGM
GVLWDGYSGVHSADLVPELMAFGGAKQERLNKEIGDVRARIYRSHLNCTV
FPNNSMLTCSGVFKVWNPIDANTTEVWTYAIVEKDMPEDLKRRLADSVQR
TFGPAGFWESDDNDNMETASQNGKKYQSRDSDLLSNLGFGEDVYGDAVYP
GVVGKSAIGETSYRGFYRAYQAHVSSSNWAEFEHASSTWHTELTKTT

3D structure

• PDB: 1ndo Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase.
• Chain: A
• Resolution: 2.25 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H104 D205 H208 H213 D362
• Catalytic site (residue number reindexed from 1): H104 D205 H208 H213 D362
• Enzyme Commision number: 1.14.12.12: naphthalene 1,2-dioxygenase.

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	FE	A	H208 H213 D362	H208 H213 D362
BS02	FES	A	C81 H83 R84 C101 Y103 H104 W106	C81 H83 R84 C101 Y103 H104 W106

Gene Ontology

Molecular Function

• GO:0005506 iron ion binding
• GO:0005515 protein binding
• GO:0018625 naphthalene 1,2-dioxygenase activity
• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity
• GO:0051537 2 iron, 2 sulfur cluster binding

Biological Process

• GO:0009056 catabolic process
• GO:0044237 cellular metabolic process

External links

• PDB: RCSB:1ndo, PDBe:1ndo, PDBj:1ndo
• PDBsum: 1ndo
• PubMed: 9634695
• UniProt: P0A110|NDOB_PSEPU Naphthalene 1,2-dioxygenase system, large oxygenase component (Gene Name=ndoB)