3EBF: Inhibited murine iNOS oxygenase domain

Structure of inhibited murine iNOS oxygenase domain. Determined by X-ray diffraction at 2.29 Å resolution. Released 7 Oct 2008.

Method: X-ray diffraction
Resolution: 2.29 Å
Organism: Mus musculus
Chains: 2
Atoms: 7,887
Mol. weight: 103 kDa
Ligands: HEM, H4B, 332
Released: 7 Oct 2008

Explore 3EBF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3EBF contains 58 α-helices and 50 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 29 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	79-82	4	1
β-strand	83	1	2
β-strand	89-92	4	1
α-helix	94-97	4
α-helix	117-119	3
β-strand	120	1	3
α-helix	127-129	3
α-helix	130-146	17
α-helix	153-170	18
α-helix	177-189	13
α-helix	197-199	3
β-strand	204-207	4	4
α-helix	214-229	16
α-helix	230-232	3
β-strand	237-240	4	4
α-helix	242-244	3
β-strand	252-253	2	5
β-strand	257	1	4
β-strand	261	1	6
β-strand	263-265	3	7
β-strand	271-273	3	7
α-helix	275-277	3
α-helix	278-286	9
α-helix	297	1
β-strand	298	1	6
α-helix	299-300	2
β-strand	301-304	4	5
α-helix	308-310	3
β-strand	311-313	3	5
α-helix	314-316	3
α-helix	317-319	3
β-strand	322-324	3	8
α-helix	331-336	6
β-strand	339-341	3	8
β-strand	345-346	2	4
β-strand	350-353	4	9
β-strand	356-358	3	9
β-strand	363-364	2	4
β-strand	367-368	2	10
α-helix	369-370	2
α-helix	371-376	6
α-helix	377-378	2
α-helix	386-392	7
α-helix	400-402	3
α-helix	404-422	19
β-strand	427-428	2	10
α-helix	430-448	19
α-helix	455-458	4
α-helix	464-466	3
α-helix	468-471	4
β-strand	472	1	2
β-strand	482-484	3	9
β-strand	485	1	3
α-helix	489-492	4

Chain B: 29 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	79-82	4	11
β-strand	83	1	12
β-strand	89-92	4	11
α-helix	94-97	4
α-helix	117-119	3
β-strand	120	1	13
α-helix	127-129	3
α-helix	130-146	17
α-helix	153-170	18
α-helix	177-189	13
α-helix	197-199	3
β-strand	204-207	4	14
α-helix	214-229	16
α-helix	230-232	3
β-strand	237-240	4	14
α-helix	241-244	4
β-strand	252-253	2	15
β-strand	257	1	14
β-strand	261	1	16
β-strand	263-265	3	17
β-strand	271-273	3	17
α-helix	275-277	3
α-helix	278-286	9
α-helix	289-291	3
α-helix	297	1
β-strand	298	1	16
α-helix	299-300	2
β-strand	301-304	4	15
α-helix	308-310	3
β-strand	311-313	3	15
α-helix	317-319	3
β-strand	322-324	3	18
α-helix	331-336	6
β-strand	339-341	3	18
β-strand	345-346	2	14
β-strand	350-353	4	19
β-strand	356-358	3	19
β-strand	363-364	2	14
β-strand	367-368	2	20
α-helix	369-370	2
α-helix	371-376	6
α-helix	377-378	2
α-helix	386-392	7
α-helix	400-402	3
α-helix	404-422	19
β-strand	427-428	2	20
α-helix	430-448	19
α-helix	455-458	4
α-helix	464-466	3
α-helix	468-471	4
β-strand	472	1	12
β-strand	482-484	3	19
β-strand	485	1	13
α-helix	489-491	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nitric oxide synthase, inducible	A, B	protein	433	Mus musculus	P29477 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3EBF_1 Nitric oxide synthase, inducible (chains A, B)
LDKLHVTSTRPQYVRIKNWGSGEILHDTLHHKATSDFTCKSKSCLGSIMNPKSLTRGPRD
KPTPLEELLPHAIEFINQYYGSFKEAKIEEHLARLEAVTKEIETTGTYQLTLDELIFATK
MAWRNAPRCIGRIQWSNLQVFDARNCSTAQEMFQHICRHILYATNNGNIRSAITVFPQRS
DGKHDFRLWNSQLIRYAGYQMPDGTIRGDAATLEFTQLCIDLGWKPRYGRFDVLPLVLQA
DGQDPEVFEIPPDLVLEVTMEHPKYEWFQELGLKWYALPAVANMLLEVGGLEFPACPFNG
WYMGTEIGVRDFCDTQRYNILEEVGRRMGLETHTLASLWKDRAVTEINVAVLHSFQKQNV
TIMDHHTASESFMKHMQNEYRARGGCPADWIWLVPPVSGSITPVFHQEMLNYVLSPFYYY
QIEPWKTHIWQNE

Ligands and cofactors

ID	Name	Formula	Copies
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	2
H4B	5,6,7,8-tetrahydrobiopterin	C9 H15 N5 O3	2
332	(3R)-3-[(1,2,3,4-tetrahydroisoquinolin-7-yloxy)methyl]-2,3-dihydrothieno[2,3-f]…	C17 H19 N3 O2 S	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Anchored plasticity opens doors for selective inhibitor design in nitric oxide synthase. Garcin, E.D., Arvai, A.S., Rosenfeld, R.J. et al. Nat Chem Biol (2008) 4:700-707. DOI 10.1038/nchembio.115 · PubMed

Other PDB entries of the same protein (UniProt P29477 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3GOF 1.45 Å, Calmodulin bound to peptide from macrophage nitric oxide synthase
2ORT 1.87 Å, Murine Inducible Nitric Oxide Synthase Oxygenase Domain (Delta 114)…
2ORP 1.97 Å, Murine inducible nitric oxide synthase oxygenase domain (delta 114)…
2ORO 2.0 Å, Murine inducible nitric oxide synthase oxygenase domain (delta 114)…
2ORR 2.0 Å, Murine Inducible Nitric Oxide Synthase Oxygenase Domain (Delta 114)…
2ORS 2.0 Å, Murine Inducible Nitric Oxide Synthase Oxygenase Domain (DELTA 114)…
3E7M 2.0 Å, Structure of murine iNOS oxygenase domain with inhibitor AR-C95791
3E65 2.05 Å, Murine INOS dimer with HEME, pterin and inhibitor AR-C120011
1NOS 2.1 Å, Murine inducible nitric oxide synthase oxygenase domain (delta 114), imidazole complex
2ORQ 2.1 Å, Murine Inducible Nitric Oxide Synthase Oxygenase Domain (DELTA 114)…
3E68 2.2 Å, Structure of murine INOS oxygenase domain with inhibitor AR-C130232
3EAI 2.2 Å, Structure of inhibited murine iNOS oxygenase domain

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