3LMM | pdb_00003lmm

Crystal Structure of the DIP2311 protein from Corynebacterium diphtheriae, Northeast Structural Genomics Consortium Target CdR35

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Winged helix DNA-binding domain	8091024	3000034	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	AlbA-like	8091021	3000507	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8091022	3000091	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	AlbA-like	8091021	3000507	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8091024	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8091022	3000091	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8091022	3000091	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	AlbA-like	8091021	3000507	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8091024	3000034	SCOP2B (2022-06-29)
A	SCOP2 Family	NE2525/DIP2311 N-terminal domain-like	8045740	4004653	SCOP2 (2022-06-29)
A	SCOP2 Family	DIP2311 ATPase-like domain-like	8049158	4006381	SCOP2 (2022-06-29)
A	SCOP2 Family	DIP2311 C-terminal domain-like	8091023	4007718	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	AlbA-like	8091021	3000507	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8091022	3000091	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8091024	3000034	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	SLFN_AlbA_2	e3lmmD1	A: a/b three-layered sandwiches	X: beta-clip	H: Schlafen 8	T: Schlafen 8	F: SLFN_AlbA_2	ECOD (v294.1)
D	HATPase_c_4	e3lmmD2	A: a/b three-layered sandwiches	X: beta-clip	H: SET domain-like	T: SET domain-like	F: HATPase_c_4	ECOD (v294.1)
D	DUF5635	e3lmmD3	A: a/b three-layered sandwiches	X: beta-clip	H: SET domain-like	T: SET domain-like	F: DUF5635	ECOD (v294.1)
D	Astacin	e3lmmD4	A: a/b three-layered sandwiches	X: beta-clip	H: SET domain-like	T: SET domain-like	F: Astacin	ECOD (v294.1)
C	HTH_20	e3lmmC4	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: HTH_20	ECOD (v294.1)
B	RVP	e3lmmB1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
A	Peptidase_C30	e3lmmA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Peptidase_C30	ECOD (v294.1)
A	Acetyltransf_1	e3lmmA4	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Acetyltransf_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.950.30	Alpha Beta	2-Layer Sandwich	Methyltransferase, Cobalt-precorrin-4 Transmethylase	Domain 2	CATH (4.3.0)
D	6.10.10.130	Special	Helix non-globular	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
D	3.30.565.60	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90		CATH (4.3.0)
D	1.10.10.2340	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
D	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C	3.30.950.30	Alpha Beta	2-Layer Sandwich	Methyltransferase, Cobalt-precorrin-4 Transmethylase	Domain 2	CATH (4.3.0)
C	6.10.10.130	Special	Helix non-globular	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	3.30.565.60	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90		CATH (4.3.0)
C	1.10.10.2340	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
B	3.30.950.30	Alpha Beta	2-Layer Sandwich	Methyltransferase, Cobalt-precorrin-4 Transmethylase	Domain 2	CATH (4.3.0)
B	6.10.10.130	Special	Helix non-globular	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	3.30.565.60	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90		CATH (4.3.0)
B	1.10.10.2340	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	3.30.950.30	Alpha Beta	2-Layer Sandwich	Methyltransferase, Cobalt-precorrin-4 Transmethylase	Domain 2	CATH (4.3.0)
A	6.10.10.130	Special	Helix non-globular	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	3.30.565.60	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90		CATH (4.3.0)
A	1.10.10.2340	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF22168	Transcriptional regulator DIP2311-like, C-terminal domain (DIP2311-like_C)	Transcriptional regulator DIP2311-like, C-terminal domain	This domain is found at the C-terminal end of Transcriptional regulator DIP2311 from Corynebacterium diphtheriae (Swiss:Q6NEG3) and similar bacterial sequences. This domain, which shows a winged helix fold, is normally found associated to Pfam:PF0432 ...	This domain is found at the C-terminal end of Transcriptional regulator DIP2311 from Corynebacterium diphtheriae (Swiss:Q6NEG3) and similar bacterial sequences. This domain, which shows a winged helix fold, is normally found associated to Pfam:PF04326.	Domain
A, B, C, D	PF13749	Putative ATP-dependent DNA helicase recG C-terminal (HATPase_c_4)	Putative ATP-dependent DNA helicase recG C-terminal	This domain may well interact selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.	Domain
A, B, C, D	PF18685	Family of unknown function (DUF5635) (DUF5635)	Family of unknown function (DUF5635)	This is a domain of unknown function which is found at the C-terminal region of Pfam:PF13749 in actinobacteria.	Domain
A, B, C, D	PF04326	Schlafen, AlbA_2 (SLFN_AlbA_2)	Schlafen, AlbA_2	This is the AlbA_2 domain from the Schlafen (SLFN) family of proteins which are important in cell differentiation and defense against viruses [1,2]. This domain is present at the N-terminal of all SLFN proteins and includes the SLFN box, a sequence u ...	This is the AlbA_2 domain from the Schlafen (SLFN) family of proteins which are important in cell differentiation and defense against viruses [1,2]. This domain is present at the N-terminal of all SLFN proteins and includes the SLFN box, a sequence unique to these proteins that may form a dimer interface [1]. The AlbA_2 domain is RNA-binding and RNase region as it contains the highly conserved catalytic glutamic acid residues [1].	Domain

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR040728	Domain of unknown function DUF5635	Domain
A, B, C, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR007421	Schlafen, AlbA_2 domain	Domain
A, B, C, D	IPR038475	RecG, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR038461	Schlafen, AlbA_2 domain superfamily	Homologous Superfamily
A, B, C, D	IPR054760	Transcriptional regulator DIP2311-like, C-terminal domain	Domain

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.