6VFS | pdb_00006vfs

ClpXP from Neisseria meningitidis - Conformation A


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
H [auth L]SCOP2B SuperfamilyClpP/crotonase 8068487 3000033 SCOP2B (2022-06-29)
I [auth O]SCOP2B SuperfamilyClpP/crotonase 8068487 3000033 SCOP2B (2022-06-29)
J [auth P]SCOP2B SuperfamilyClpP/crotonase 8068487 3000033 SCOP2B (2022-06-29)
K [auth Q]SCOP2B SuperfamilyClpP/crotonase 8068487 3000033 SCOP2B (2022-06-29)
L [auth R]SCOP2B SuperfamilyClpP/crotonase 8068487 3000033 SCOP2B (2022-06-29)
M [auth S]SCOP2B SuperfamilyClpP/crotonase 8068487 3000033 SCOP2B (2022-06-29)
N [auth T]SCOP2B SuperfamilyClpP/crotonase 8068487 3000033 SCOP2B (2022-06-29)
O [auth U]SCOP2B SuperfamilyClpP/crotonase 8068487 3000033 SCOP2B (2022-06-29)
P [auth H]SCOP2B SuperfamilyClpP/crotonase 8068487 3000033 SCOP2B (2022-06-29)
Q [auth I]SCOP2B SuperfamilyClpP/crotonase 8068487 3000033 SCOP2B (2022-06-29)
R [auth J]SCOP2B SuperfamilyClpP/crotonase 8068487 3000033 SCOP2B (2022-06-29)
S [auth K]SCOP2B SuperfamilyClpP/crotonase 8068487 3000033 SCOP2B (2022-06-29)
T [auth M]SCOP2B SuperfamilyClpP/crotonase 8068487 3000033 SCOP2B (2022-06-29)
U [auth N]SCOP2B SuperfamilyClpP/crotonase 8068487 3000033 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth E]ClpB_D2-smalle6vfsE2 A: alpha arraysX: Histone-likeH: Histone-relatedT: AAA+ ATPase lid domainF: ClpB_D2-smallECOD (1.6)
A [auth E]Sigma54_activate6vfsE1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: Sigma54_activatECOD (1.6)
B [auth A]ClpB_D2-smalle6vfsA1 A: alpha arraysX: Histone-likeH: Histone-relatedT: AAA+ ATPase lid domainF: ClpB_D2-smallECOD (1.6)
B [auth A]Sigma54_activate6vfsA2 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: Sigma54_activatECOD (1.6)
C [auth F]ClpB_D2-smalle6vfsF1 A: alpha arraysX: Histone-likeH: Histone-relatedT: AAA+ ATPase lid domainF: ClpB_D2-smallECOD (1.6)
C [auth F]Sigma54_activate6vfsF2 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: Sigma54_activatECOD (1.6)
D [auth C]ClpB_D2-smalle6vfsC1 A: alpha arraysX: Histone-likeH: Histone-relatedT: AAA+ ATPase lid domainF: ClpB_D2-smallECOD (1.6)
D [auth C]Sigma54_activate6vfsC2 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: Sigma54_activatECOD (1.6)
E [auth B]ClpB_D2-smalle6vfsB1 A: alpha arraysX: Histone-likeH: Histone-relatedT: AAA+ ATPase lid domainF: ClpB_D2-smallECOD (1.6)
E [auth B]Sigma54_activate6vfsB2 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: Sigma54_activatECOD (1.6)
F [auth D]ClpB_D2-smalle6vfsD2 A: alpha arraysX: Histone-likeH: Histone-relatedT: AAA+ ATPase lid domainF: ClpB_D2-smallECOD (1.6)
F [auth D]Sigma54_activate6vfsD1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: Sigma54_activatECOD (1.6)
H [auth L]CLP_proteasee6vfsL1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: CLP_proteaseECOD (1.6)
I [auth O]CLP_proteasee6vfsO1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: CLP_proteaseECOD (1.6)
J [auth P]CLP_proteasee6vfsP1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: CLP_proteaseECOD (1.6)
K [auth Q]CLP_proteasee6vfsQ1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: CLP_proteaseECOD (1.6)
L [auth R]CLP_proteasee6vfsR1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: CLP_proteaseECOD (1.6)
M [auth S]CLP_proteasee6vfsS1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: CLP_proteaseECOD (1.6)
N [auth T]CLP_proteasee6vfsT1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: CLP_proteaseECOD (1.6)
O [auth U]CLP_proteasee6vfsU1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: CLP_proteaseECOD (1.6)
P [auth H]CLP_proteasee6vfsH1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: CLP_proteaseECOD (1.6)
Q [auth I]CLP_proteasee6vfsI1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: CLP_proteaseECOD (1.6)
R [auth J]CLP_proteasee6vfsJ1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: CLP_proteaseECOD (1.6)
S [auth K]CLP_proteasee6vfsK1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: CLP_proteaseECOD (1.6)
T [auth M]CLP_proteasee6vfsM1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: CLP_proteaseECOD (1.6)
U [auth N]CLP_proteasee6vfsN1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: CLP_proteaseECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A [auth E]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
A [auth E]1.10.8.60 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3CATH (utative)
B [auth A]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
B [auth A]1.10.8.60 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3CATH (utative)
C [auth F]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
C [auth F]1.10.8.60 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3CATH (utative)
D [auth C]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
D [auth C]1.10.8.60 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3CATH (utative)
E [auth B]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
E [auth B]1.10.8.60 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3CATH (utative)
F [auth D]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
F [auth D]1.10.8.60 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3CATH (utative)
H [auth L]3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (utative)
I [auth O]3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (utative)
J [auth P]3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (utative)
K [auth Q]3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (utative)
L [auth R]3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (utative)
M [auth S]3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (utative)
N [auth T]3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (utative)
O [auth U]3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (utative)
P [auth H]3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (utative)
Q [auth I]3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (utative)
R [auth J]3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (utative)
S [auth K]3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (utative)
T [auth M]3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (utative)
U [auth N]3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (utative)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF10431C-terminal, D2-small domain, of ClpB protein (ClpB_D2-small)C-terminal, D2-small domain, of ClpB proteinThis is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, Pfam:PF00004) it lacks the long coiled-coil insertion, and instead of helix C4 ...This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, Pfam:PF00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilise the functional assembly [1]. The domain is associated with two Clp_N, Pfam:PF02861, at the N-terminus as well as AAA, Pfam:PF00004 and AAA_2, Pfam:PF07724.
Domain
PF07724AAA domain (Cdc48 subfamily) (AAA_2)AAA domain (Cdc48 subfamily)This Pfam entry includes some of the AAA proteins not detected by the Pfam:PF00004 model. Domain
PF00574Clp protease (CLP_protease)Clp proteaseThe Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. Swiss:P48254 has lost all of these active site residues and is therefore inactive. Swiss:P42379 contains two large in ...The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. Swiss:P48254 has lost all of these active site residues and is therefore inactive. Swiss:P42379 contains two large insertions, Swiss:P42380 contains one large insertion.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
ATP-dependent Clp protease ATP-binding subunit ClpX
Unidentified protein substrate---
ATP-dependent Clp protease proteolytic subunit

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR050052ATP-dependent Clp protease ATP-binding subunit ClpXFamily
IPR046425Clp protease, ATP-binding subunit ClpX, bacteriaFamily
IPR004487Clp protease, ATP-binding subunit ClpXFamily
IPR010603Zinc finger, ClpX C4-typeDomain
IPR003593AAA+ ATPase domainDomain
IPR003959ATPase, AAA-type, coreDomain
IPR019489Clp ATPase, C-terminalDomain
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
IPR038366Zinc finger, ClpX C4-type superfamilyHomologous Superfamily
IPR029045ClpP/crotonase-like domain superfamilyHomologous Superfamily
IPR001907ATP-dependent Clp protease proteolytic subunitFamily
IPR018215ClpP, Ser active siteActive Site
IPR033135ClpP, histidine active siteActive Site
IPR023562Clp protease proteolytic subunit /Translocation-enhancing protein TepAFamily