1YEW | pdb_00001yew

Crystal structure of particulate methane monooxygenase

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I [auth K]	SCOP2B Superfamily	Ammonia monooxygenase/methane monooxygenase, subunit C-like	8053445	3002188	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	Ammonia monooxygenase/methane monooxygenase, subunit C-like	8053445	3002188	SCOP2B (2022-06-29)
C	SCOP2 Family	Ammonia monooxygenase/methane monooxygenase, subunit C-like	8046644	4005211	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Ammonia monooxygenase/methane monooxygenase, subunit C-like	8053445	3002188	SCOP2 (2022-06-29)
H [auth J]	SCOP2B Superfamily	Gx transporter-like	8095951	3002268	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	Gx transporter-like	8095951	3002268	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Gx transporter-like	8095951	3002268	SCOP2B (2022-06-29)
G [auth I]	SCOP2B Superfamily	Monooxygenase subunit B C-terminal domain-like	8095935	3002712	SCOP2B (2022-06-29)
G [auth I]	SCOP2B Superfamily	PapD-like	8095933	3002067	SCOP2B (2022-06-29)
G [auth I]	SCOP2B Superfamily	Monooxygenase subunit B transmembrane domain-like	8095934	3002711	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	PapD-like	8095933	3002067	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Monooxygenase subunit B transmembrane domain-like	8095934	3002711	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Monooxygenase subunit B C-terminal domain-like	8095935	3002712	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Monooxygenase subunit B C-terminal domain-like	8095935	3002712	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PapD-like	8095933	3002067	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Monooxygenase subunit B transmembrane domain-like	8095934	3002711	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
I [auth K]	7kD_DNA_binding	e1yewK1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: 7kD_DNA_binding	ECOD (v294.1)
F [auth G]	7kD_DNA_binding	e1yewG1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: 7kD_DNA_binding	ECOD (v294.1)
C	AmoC	e1yewC1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: HTH	T: Ribbon-helix-helix	F: AmoC	ECOD (v294.1)
H [auth J]	7kD_DNA_binding	e1yewJ1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: 7kD_DNA_binding	ECOD (v294.1)
E [auth F]	7kD_DNA_binding	e1yewF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: 7kD_DNA_binding	ECOD (v294.1)
B	7kD_DNA_binding	e1yewB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: 7kD_DNA_binding	ECOD (v294.1)
G [auth I]	CagX	e1yewI1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: CagX	ECOD (v294.1)
D [auth E]	CagX	e1yewE1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: CagX	ECOD (v294.1)
A	CagX	e1yewA1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: CagX	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I [auth K]	1.20.1050.50	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)
F [auth G]	1.20.1050.50	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)
C	1.20.1050.50	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)
H [auth J]	1.20.1450.10	Mainly Alpha	Up-down Bundle	particulate methane monooxygenase, chain B	Ammonia/particulate methane monooxygenase, subunit A	CATH (4.3.0)
E [auth F]	1.20.1450.10	Mainly Alpha	Up-down Bundle	particulate methane monooxygenase, chain B	Ammonia/particulate methane monooxygenase, subunit A	CATH (4.3.0)
B	1.20.1450.10	Mainly Alpha	Up-down Bundle	particulate methane monooxygenase, chain B	Ammonia/particulate methane monooxygenase, subunit A	CATH (4.3.0)
G [auth I]	2.60.120.570	Mainly Beta	Sandwich	Jelly Rolls	Particulate methane monooxygenase, b subunit. Chain: A, domain 1	CATH (4.3.0)
G [auth I]	1.10.287.710	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
G [auth I]	2.60.40.1580	Mainly Beta	Sandwich	Immunoglobulin-like	Particulate methane monooxygenase, b subunit. Chain: A, domain 3	CATH (4.3.0)
D [auth E]	2.60.120.570	Mainly Beta	Sandwich	Jelly Rolls	Particulate methane monooxygenase, b subunit. Chain: A, domain 1	CATH (4.3.0)
D [auth E]	1.10.287.710	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
D [auth E]	2.60.40.1580	Mainly Beta	Sandwich	Immunoglobulin-like	Particulate methane monooxygenase, b subunit. Chain: A, domain 3	CATH (4.3.0)
A	2.60.120.570	Mainly Beta	Sandwich	Jelly Rolls	Particulate methane monooxygenase, b subunit. Chain: A, domain 1	CATH (4.3.0)
A	1.10.287.710	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
A	2.60.40.1580	Mainly Beta	Sandwich	Immunoglobulin-like	Particulate methane monooxygenase, b subunit. Chain: A, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, E [auth F], H [auth J]	PF02461	Ammonia monooxygenase (AMO)	Ammonia monooxygenase	-	Family
A, D [auth E], G [auth I]	PF04744	Monooxygenase subunit B protein (Monooxygenase_B)	Monooxygenase subunit B protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F [auth G], I [auth K]	particulate methane monooxygenase subunit C2	monooxygenase activity oxidoreductase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	-	-
B, E [auth F], H [auth J]	particulate methane monooxygenase, A subunit	monooxygenase activity oxidoreductase activity catalytic activity	-	cellular anatomical structure membrane
A, D [auth E], G [auth I]	particulate methane monooxygenase, B subunit	monooxygenase activity oxidoreductase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	-	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F [auth G], I [auth K]	IPR006980	Ammonia monooxygenase/particulate methane monooxygenase, subunit C	Family
C, F [auth G], I [auth K]	IPR023349	Ammonia monooxygenase/particulate methane monooxygenase, subunit C domain superfamily	Homologous Superfamily
B, E [auth F], H [auth J]	IPR037001	Ammonia/particulate methane monooxygenase, subunit A superfamily	Homologous Superfamily
B, E [auth F], H [auth J]	IPR003393	Ammonia monooxygenase/particulate methane monooxygenase, subunit A	Family
A, D [auth E], G [auth I]	IPR006833	Ammonia monooxygenase/particulate methane monooxygenase, subunit B	Family
A, D [auth E], G [auth I]	IPR023141	Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily	Homologous Superfamily
A, D [auth E], G [auth I]	IPR023303	Ammonia/methane monooxygenase, subunit B, C-terminal	Homologous Superfamily
A, D [auth E], G [auth I]	IPR023301	Ammonia/methane monooxygenase, subunitB, N-terminal	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D [auth E], E [auth F] A, B, C, D [auth E], E [auth F], F [auth G], G [auth I], H [auth J], I [auth K]	OPM	Transmembrane	Alpha-helical polytopic	Methane monooxygenase	Methane monooxygenase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D [auth E], E [auth F] A, B, C, D [auth E], E [auth F], F [auth G], G [auth I], H [auth J], I [auth K]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D [auth E], E [auth F] A, B, C, D [auth E], E [auth F], F [auth G], G [auth I], H [auth J], I [auth K]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D [auth E], E [auth F] A, B, C, D [auth E], E [auth F], F [auth G], G [auth I], H [auth J], I [auth K]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Oxygenases	Particulate methane monooxgenase (pMMO)

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.