3RGB | pdb_00003rgb

Crystal structure of particulate methane monooxygenase from Methylococcus capsulatus (Bath)

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth J]	SCOP2 Family	Ammonia monooxygenase-like	8050418	4006879	SCOP2 (2022-06-29)
F [auth J]	SCOP2 Superfamily	Gx transporter-like	8095951	3002268	SCOP2 (2022-06-29)
G [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)
C	SCOP2 Family	Ammonia monooxygenase/methane monooxygenase, subunit C-like	8046643	4005211	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Ammonia monooxygenase/methane monooxygenase, subunit C-like	8053446	3002188	SCOP2 (2022-06-29)
H [auth K]	SCOP2B Superfamily	Ammonia monooxygenase/methane monooxygenase, subunit C-like	8053446	3002188	SCOP2B (2022-06-29)
I [auth G]	SCOP2B Superfamily	Ammonia monooxygenase/methane monooxygenase, subunit C-like	8053446	3002188	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PapD-like	8095933	3002067	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Monooxygenase subunit B C-terminal domain-like	8095935	3002712	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Monooxygenase subunit B transmembrane domain-like	8095934	3002711	SCOP2B (2022-06-29)
E [auth I]	SCOP2 Family	Monooxygenase subunit B copper-binding domain-like	8046391	4005056	SCOP2 (2022-06-29)
E [auth I]	SCOP2 Family	Monooxygenase subunit B transmembrane domain-like	8095931	4007811	SCOP2 (2022-06-29)
E [auth I]	SCOP2 Family	Monooxygenase subunit B C-terminal domain-like	8095932	4007812	SCOP2 (2022-06-29)
E [auth I]	SCOP2 Superfamily	PapD-like	8095933	3002067	SCOP2 (2022-06-29)
E [auth I]	SCOP2 Superfamily	Monooxygenase subunit B transmembrane domain-like	8095934	3002711	SCOP2 (2022-06-29)
E [auth I]	SCOP2 Superfamily	Monooxygenase subunit B C-terminal domain-like	8095935	3002712	SCOP2 (2022-06-29)
D [auth E]	SCOP2B Superfamily	PapD-like	8095933	3002067	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Monooxygenase subunit B C-terminal domain-like	8095935	3002712	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Monooxygenase subunit B transmembrane domain-like	8095934	3002711	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth J]	e3rgbJ1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: PK_Tyr_Ser-Thr	F:	ECOD (20:10:01)
G [auth F]	e3rgbF1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: PK_Tyr_Ser-Thr	F:	ECOD (20:10:01)
B	e3rgbB1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: PK_Tyr_Ser-Thr	F:	ECOD (20:10:01)
C	e3rgbC1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: ADAM_CR	F:	ECOD (20:10:01)
H [auth K]	e3rgbK1	A: jelly-roll	X: Double-stranded beta-helix	H: Double-stranded beta-helix	T: zf-MYND	F:	ECOD (20:10:01)
I [auth G]	e3rgbG1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: ADAM_CR	F:	ECOD (20:10:01)
A	e3rgbA1	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: CagX	F:	ECOD (20:10:01)
E [auth I]	e3rgbI1	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: CagX	F:	ECOD (20:10:01)
D [auth E]	e3rgbE1	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: CagX	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, F [auth J], G [auth F]	PF02461	Ammonia monooxygenase (AMO)	Ammonia monooxygenase	-	Family
A, D [auth E], E [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
B, F [auth J], G [auth F]	Methane monooxygenase subunit A2	monooxygenase activity oxidoreductase activity catalytic activity	-	cellular anatomical structure membrane
C, H [auth K], I [auth G]	Methane monooxygenase subunit C2	oxidoreductase activity monooxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen methane monooxygenase [NAD(P)H] activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen catalytic activity cation binding ion binding binding metal ion binding small molecule binding	-	-
A, D [auth E], E [auth I]	Methane monooxygenase subunit B2	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
B, F [auth J], G [auth F]	IPR037001	Ammonia/particulate methane monooxygenase, subunit A superfamily	Homologous Superfamily
B, F [auth J], G [auth F]	IPR003393	Ammonia monooxygenase/particulate methane monooxygenase, subunit A	Family
C, H [auth K], I [auth G]	IPR006980	Ammonia monooxygenase/particulate methane monooxygenase, subunit C	Family
C, H [auth K], I [auth G]	IPR023349	Ammonia monooxygenase/particulate methane monooxygenase, subunit C domain superfamily	Homologous Superfamily
A, D [auth E], E [auth I]	IPR006833	Ammonia monooxygenase/particulate methane monooxygenase, subunit B	Family
A, D [auth E], E [auth I]	IPR023141	Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily	Homologous Superfamily
A, D [auth E], E [auth I]	IPR023303	Ammonia/methane monooxygenase, subunit B, C-terminal	Homologous Superfamily
A, D [auth E], E [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 I] A, B, C, D [auth E], E [auth I], F [auth J], G [auth F], H [auth K], I [auth G]	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 I] A, B, C, D [auth E], E [auth I], F [auth J], G [auth F], H [auth K], I [auth G]	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 I] A, B, C, D [auth E], E [auth I], F [auth J], G [auth F], H [auth K], I [auth G]	MemProtMD	Annotated as membrane protein by MemProtMD