6Q2D | pdb_00006q2d

Crystal structure of Methanobrevibacter smithii Dph2 in complex with Methanobrevibacter smithii elongation factor 2

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth F]	EFG_IV	e6q2dF3	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: EFG_IV	ECOD (1.6)
D [auth F]	EFG_C	e6q2dF1	A: a+b two layers	X: Alpha-beta plaits	H: EF-G C-terminal domain-like (From Topology)	T: EF-G C-terminal domain-like	F: EFG_C	ECOD (1.6)
D [auth F]	EFG_II	e6q2dF2	A: a+b two layers	X: Alpha-beta plaits	H: EF-G C-terminal domain-like (From Topology)	T: EF-G C-terminal domain-like	F: EFG_II	ECOD (1.6)
C	GTP_EFTU_D2	e6q2dC4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2	ECOD (1.6)
C	EFG_IV	e6q2dC2	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: EFG_IV	ECOD (1.6)
C	EFG_C	e6q2dC1	A: a+b two layers	X: Alpha-beta plaits	H: EF-G C-terminal domain-like (From Topology)	T: EF-G C-terminal domain-like	F: EFG_C	ECOD (1.6)
C	EFG_II	e6q2dC5	A: a+b two layers	X: Alpha-beta plaits	H: EF-G C-terminal domain-like (From Topology)	T: EF-G C-terminal domain-like	F: EFG_II	ECOD (1.6)
C	MnmE_helical_2nd	e6q2dC3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)
B	Diphthamide_syn_3rd	e6q2dB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Iron-sulphur enzyme Dph2	F: Diphthamide_syn_3rd	ECOD (1.6)
B	Diphthamide_syn_2nd	e6q2dB3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Iron-sulphur enzyme Dph2	F: Diphthamide_syn_2nd	ECOD (1.6)
B	Diphthamide_syn_1st	e6q2dB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Iron-sulphur enzyme Dph2	F: Diphthamide_syn_1st	ECOD (1.6)
A	Diphthamide_syn_3rd	e6q2dA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Iron-sulphur enzyme Dph2	F: Diphthamide_syn_3rd	ECOD (1.6)
A	Diphthamide_syn_2nd	e6q2dA3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Iron-sulphur enzyme Dph2	F: Diphthamide_syn_2nd	ECOD (1.6)
A	Diphthamide_syn_1st	e6q2dA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Iron-sulphur enzyme Dph2	F: Diphthamide_syn_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
C	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (utative)
C	3.30.70.870	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Elongation Factor G (Translational Gtpase), domain 3	CATH (utative)
C	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (utative)
B	3.40.50.11840	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Diphthamide synthesis DPH1/DPH2 domain 1	CATH (utative)
B	3.40.50.11850	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Diphthamide synthesis DPH1/DPH2 domain 2	CATH (utative)
B	3.40.50.11860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Diphthamide synthesis DPH1/DPH2 domain 3	CATH (utative)
A	3.40.50.11840	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Diphthamide synthesis DPH1/DPH2 domain 1	CATH (utative)
A	3.40.50.11850	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Diphthamide synthesis DPH1/DPH2 domain 2	CATH (utative)
A	3.40.50.11860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Diphthamide synthesis DPH1/DPH2 domain 3	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D [auth F]	PF00679	Elongation factor G C-terminus (EFG_C)	Elongation factor G C-terminus	This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold.	Domain
C, D [auth F]	PF00009	Elongation factor Tu GTP binding domain (GTP_EFTU)	Elongation factor Tu GTP binding domain	This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.	Domain
C, D [auth F]	PF14492	Elongation Factor G, domain III (EFG_III)	Elongation Factor G, domain III	This domain is found in Elongation Factor G. It shares a similar structure with domain V (Pfam:PF00679). Structural studies in drosophila indicate this is domain 3 [1].	Domain
C, D [auth F]	PF03144	Elongation factor Tu domain 2 (GTP_EFTU_D2)	Elongation factor Tu domain 2	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ...	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain.	Domain
C, D [auth F]	PF03764	Elongation factor G, domain IV (EFG_IV)	Elongation factor G, domain IV	This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold.	Domain
A, B	PF01866	Putative diphthamide synthesis protein (Diphthamide_syn)	Putative diphthamide synthesis protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D [auth F]	Elongation factor 2	translation factor activity translation elongation factor activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding translation factor activity translation elongation factor activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex ribonucleoprotein complex
A, B	2-(3-amino-3-carboxypropyl)histidine synthase	2-(3-amino-3-carboxypropyl)histidine synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	peptidyl-histidine modification macromolecule modification peptidyl-amino acid modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process protein histidyl modification to diphthamide	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D [auth F]	IPR005225	Small GTP-binding domain	Domain
C, D [auth F]	IPR005517	Translation elongation factor EFG/EF2, domain IV	Domain
C, D [auth F]	IPR004543	Translation elongation factor EFG/EF2, archaeal	Family
C, D [auth F]	IPR000795	Translational (tr)-type GTP-binding domain	Domain
C, D [auth F]	IPR000640	Elongation factor EFG, domain V-like	Domain
C, D [auth F]	IPR031157	Tr-type G domain, conserved site	Conserved Site
C, D [auth F]	IPR035647	EF-G domain III/V-like	Homologous Superfamily
C, D [auth F]	IPR041095	Elongation Factor G, domain II	Domain
C, D [auth F]	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
C, D [auth F]	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
C, D [auth F]	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
C, D [auth F]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C, D [auth F]	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily
A, B	IPR042265	Diphthamide synthesis DPH1/DPH2, domain 3	Homologous Superfamily
A, B	IPR022428	Diphthamide synthesis Dph2, archaea	Family
A, B	IPR042263	Diphthamide synthesis DPH1/DPH2, domain 1	Homologous Superfamily
A, B	IPR042264	Diphthamide synthesis DPH1/DPH2, domain 2	Homologous Superfamily
A, B	IPR016435	Diphthamide synthesis DPH1/DPH2	Family
A, B	IPR035435	Diphthamide synthesis DHP1/DPH2, eukaryotes and archaea	Family

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.