6RXM

Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8041390	3001728	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8041390	3001728	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8041390	3001728	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8041390	3001728	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8041390	3001728	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8041390	3001728	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)
A	PF02146	e6rxmA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF02146	ECOD (1.6)
A	F_UNCLASSIFIED	e6rxmA1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF02146	e6rxmB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF02146	ECOD (1.6)
B	F_UNCLASSIFIED	e6rxmB2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)
C	PF02146	e6rxmC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF02146	ECOD (1.6)
C	F_UNCLASSIFIED	e6rxmC1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF02146	e6rxmD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF02146	ECOD (1.6)
D	F_UNCLASSIFIED	e6rxmD1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)
F	PF02146	e6rxmF2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF02146	ECOD (1.6)
F	F_UNCLASSIFIED	e6rxmF1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)
E	PF02146	e6rxmE2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF02146	ECOD (1.6)
E	F_UNCLASSIFIED	e6rxmE1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
A	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (utative)
B	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
B	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (utative)
C	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
D	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
F	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
F	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (utative)
E	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF02146	Sir2 family (SIR2)	Sir2 family	-	Family
G, H, I, J, K G, H, I, J, K, L	PF15511	Centromere kinetochore component CENP-T histone fold (CENP-T_C)	Centromere kinetochore component CENP-T histone fold	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	NAD-dependent protein deacylase	acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity NAD-dependent protein de-2-hydroxyisobutyrylase activity catalytic activity NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity NAD-dependent protein de-2-hydroxyisobutyrylase activity catalytic activity NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity protein-succinyllysine desuccinylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds guanyl nucleotide binding cyclic nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding cyclic-di-GMP binding carbohydrate derivative binding ribonucleotide binding NAD+ ADP-ribosyltransferase activity pentosyltransferase activity glycosyltransferase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein NAD-dependent protein lysine deacetylase activity protein-malonyllysine demalonylase activity lipoamidase activity cation binding transition metal ion binding zinc ion binding metal ion binding NAD-dependent histone deacetylase activity histone deacetylase activity histone modifying activity	chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to biotic stimulus defense response to virus defense response to other organism response to stress chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to biotic stimulus defense response to virus defense response to other organism response to stress response to external biotic stimulus response to virus	intracellular anatomical structure cytoplasm cellular anatomical entity
G, H, I, J, K G, H, I, J, K, L	Histone H4	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I rRNA transcription organic substance biosynthetic process rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I cellular metabolic process primary metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I rRNA transcription organic substance biosynthetic process rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process ncRNA metabolic process metabolic process cellular process macromolecule metabolic process protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular component organization or biogenesis nucleosome assembly nucleosome organization regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of transcription by RNA polymerase I positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle RNA polymerase I upstream activating factor complex RNA polymerase I transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle RNA polymerase I upstream activating factor complex RNA polymerase I transcription regulator complex organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle replication fork protection complex nuclear replication fork nuclear chromosome chromosome replication fork protein-DNA complex nucleosome chromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR027546	Sirtuin, class III	Family
A, B, C, D, E A, B, C, D, E, F	IPR026590	Sirtuin family, catalytic core domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR026591	Sirtuin, catalytic core small domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR003000	Sirtuin family	Family
A, B, C, D, E A, B, C, D, E, F	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR009072	Histone-fold	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR035425	CENP-T/Histone H4, histone fold	Domain
G, H, I, J, K G, H, I, J, K, L	IPR001951	Histone H4	Family
G, H, I, J, K G, H, I, J, K, L	IPR019809	Histone H4, conserved site	Conserved Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
G, H, I, J, K G, H, I, J, K, L	ALY	Parent Component: LYS RESID: AA0055 PSI-MOD : N6-acetyl-L-lysine MOD:00064

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 R01GM133198.