4MTK | pdb_00004mtk

Crystal structure of PA0091 VgrG1, the central spike of the Type VI Secretion System


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APhage_GPD_1ste4mtkA1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Phage tail proteinsF: Phage_GPD_1stECOD (1.6)
APhage_GPD_4the4mtkA3 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Phage tail proteinsF: Phage_GPD_4thECOD (1.6)
APhage_base_Ve4mtkA5 A: beta barrelsX: OB-foldH: Tail-associated lysozyme gp5-N (From Topology)T: Tail-associated lysozyme gp5-NF: Phage_base_VECOD (1.6)
AVI_Rhs_Vgre4mtkA6 A: beta duplicates or obligate multimersX: Phage tail fiber protein trimerization domain (From Topology)H: Phage tail fiber protein trimerization domain (From Topology)T: Phage tail fiber protein trimerization domainF: VI_Rhs_VgrECOD (1.6)
APhage_GPD_2nde4mtkA2 A: a+b complex topologyX: N0 domain in phage tail proteins and secretins-likeH: N0 domain in phage tail proteins and secretins (From Topology)T: N0 domain in phage tail proteins and secretinsF: Phage_GPD_2ndECOD (1.6)
APhage_GPD_3rde4mtkA4 A: a+b complex topologyX: C-terminal insertion domain in phage tail proteins (From Topology)H: C-terminal insertion domain in phage tail proteins (From Topology)T: C-terminal insertion domain in phage tail proteinsF: Phage_GPD_3rdECOD (1.6)
BPhage_GPD_1ste4mtkB4 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Phage tail proteinsF: Phage_GPD_1stECOD (1.6)
BPhage_GPD_4the4mtkB5 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Phage tail proteinsF: Phage_GPD_4thECOD (1.6)
BPhage_base_Ve4mtkB2 A: beta barrelsX: OB-foldH: Tail-associated lysozyme gp5-N (From Topology)T: Tail-associated lysozyme gp5-NF: Phage_base_VECOD (1.6)
BVI_Rhs_Vgre4mtkB6 A: beta duplicates or obligate multimersX: Phage tail fiber protein trimerization domain (From Topology)H: Phage tail fiber protein trimerization domain (From Topology)T: Phage tail fiber protein trimerization domainF: VI_Rhs_VgrECOD (1.6)
BPhage_GPD_2nde4mtkB3 A: a+b complex topologyX: N0 domain in phage tail proteins and secretins-likeH: N0 domain in phage tail proteins and secretins (From Topology)T: N0 domain in phage tail proteins and secretinsF: Phage_GPD_2ndECOD (1.6)
BPhage_GPD_3rde4mtkB7 A: a+b complex topologyX: C-terminal insertion domain in phage tail proteins (From Topology)H: C-terminal insertion domain in phage tail proteins (From Topology)T: C-terminal insertion domain in phage tail proteinsF: Phage_GPD_3rdECOD (1.6)
CPhage_GPD_1ste4mtkC4 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Phage tail proteinsF: Phage_GPD_1stECOD (1.6)
CPhage_GPD_4the4mtkC5 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Phage tail proteinsF: Phage_GPD_4thECOD (1.6)
CPhage_base_Ve4mtkC2 A: beta barrelsX: OB-foldH: Tail-associated lysozyme gp5-N (From Topology)T: Tail-associated lysozyme gp5-NF: Phage_base_VECOD (1.6)
CVI_Rhs_Vgre4mtkC6 A: beta duplicates or obligate multimersX: Phage tail fiber protein trimerization domain (From Topology)H: Phage tail fiber protein trimerization domain (From Topology)T: Phage tail fiber protein trimerization domainF: VI_Rhs_VgrECOD (1.6)
CPhage_GPD_2nde4mtkC3 A: a+b complex topologyX: N0 domain in phage tail proteins and secretins-likeH: N0 domain in phage tail proteins and secretins (From Topology)T: N0 domain in phage tail proteins and secretinsF: Phage_GPD_2ndECOD (1.6)
CPhage_GPD_3rde4mtkC7 A: a+b complex topologyX: C-terminal insertion domain in phage tail proteins (From Topology)H: C-terminal insertion domain in phage tail proteins (From Topology)T: C-terminal insertion domain in phage tail proteinsF: Phage_GPD_3rdECOD (1.6)
DPhage_GPD_1ste4mtkD4 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Phage tail proteinsF: Phage_GPD_1stECOD (1.6)
DPhage_GPD_4the4mtkD5 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Phage tail proteinsF: Phage_GPD_4thECOD (1.6)
DPhage_base_Ve4mtkD2 A: beta barrelsX: OB-foldH: Tail-associated lysozyme gp5-N (From Topology)T: Tail-associated lysozyme gp5-NF: Phage_base_VECOD (1.6)
DVI_Rhs_Vgre4mtkD1 A: beta duplicates or obligate multimersX: Phage tail fiber protein trimerization domain (From Topology)H: Phage tail fiber protein trimerization domain (From Topology)T: Phage tail fiber protein trimerization domainF: VI_Rhs_VgrECOD (1.6)
DPhage_GPD_2nde4mtkD3 A: a+b complex topologyX: N0 domain in phage tail proteins and secretins-likeH: N0 domain in phage tail proteins and secretins (From Topology)T: N0 domain in phage tail proteins and secretinsF: Phage_GPD_2ndECOD (1.6)
DPhage_GPD_3rde4mtkD6 A: a+b complex topologyX: C-terminal insertion domain in phage tail proteins (From Topology)H: C-terminal insertion domain in phage tail proteins (From Topology)T: C-terminal insertion domain in phage tail proteinsF: Phage_GPD_3rdECOD (1.6)
EPhage_GPD_1ste4mtkE4 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Phage tail proteinsF: Phage_GPD_1stECOD (1.6)
EPhage_GPD_4the4mtkE5 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Phage tail proteinsF: Phage_GPD_4thECOD (1.6)
EPhage_base_Ve4mtkE2 A: beta barrelsX: OB-foldH: Tail-associated lysozyme gp5-N (From Topology)T: Tail-associated lysozyme gp5-NF: Phage_base_VECOD (1.6)
EVI_Rhs_Vgre4mtkE1 A: beta duplicates or obligate multimersX: Phage tail fiber protein trimerization domain (From Topology)H: Phage tail fiber protein trimerization domain (From Topology)T: Phage tail fiber protein trimerization domainF: VI_Rhs_VgrECOD (1.6)
EPhage_GPD_2nde4mtkE3 A: a+b complex topologyX: N0 domain in phage tail proteins and secretins-likeH: N0 domain in phage tail proteins and secretins (From Topology)T: N0 domain in phage tail proteins and secretinsF: Phage_GPD_2ndECOD (1.6)
EPhage_GPD_3rde4mtkE6 A: a+b complex topologyX: C-terminal insertion domain in phage tail proteins (From Topology)H: C-terminal insertion domain in phage tail proteins (From Topology)T: C-terminal insertion domain in phage tail proteinsF: Phage_GPD_3rdECOD (1.6)
FPhage_GPD_1ste4mtkF4 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Phage tail proteinsF: Phage_GPD_1stECOD (1.6)
FPhage_GPD_4the4mtkF5 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Phage tail proteinsF: Phage_GPD_4thECOD (1.6)
FPhage_base_Ve4mtkF2 A: beta barrelsX: OB-foldH: Tail-associated lysozyme gp5-N (From Topology)T: Tail-associated lysozyme gp5-NF: Phage_base_VECOD (1.6)
FVI_Rhs_Vgre4mtkF1 A: beta duplicates or obligate multimersX: Phage tail fiber protein trimerization domain (From Topology)H: Phage tail fiber protein trimerization domain (From Topology)T: Phage tail fiber protein trimerization domainF: VI_Rhs_VgrECOD (1.6)
FPhage_GPD_2nde4mtkF3 A: a+b complex topologyX: N0 domain in phage tail proteins and secretins-likeH: N0 domain in phage tail proteins and secretins (From Topology)T: N0 domain in phage tail proteins and secretinsF: Phage_GPD_2ndECOD (1.6)
FPhage_GPD_3rde4mtkF6 A: a+b complex topologyX: C-terminal insertion domain in phage tail proteins (From Topology)H: C-terminal insertion domain in phage tail proteins (From Topology)T: C-terminal insertion domain in phage tail proteinsF: Phage_GPD_3rdECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A2.30.110.50 Mainly Beta Roll Pnp Oxidase Chain ACATH (4.3.0)
A3.55.50.10 Alpha Beta 3-Layer(bab) Sandwich Phage tail protein beta-alpha-beta fold Baseplate protein-like domainsCATH (4.3.0)
A4.10.220.110 Few Secondary Structures Irregular Light-harvesting Protein CATH (4.3.0)
A2.40.50.230 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Gp5 N-terminal domainCATH (4.3.0)
B2.30.110.50 Mainly Beta Roll Pnp Oxidase Chain ACATH (4.3.0)
B3.55.50.10 Alpha Beta 3-Layer(bab) Sandwich Phage tail protein beta-alpha-beta fold Baseplate protein-like domainsCATH (4.3.0)
B4.10.220.110 Few Secondary Structures Irregular Light-harvesting Protein CATH (4.3.0)
B2.40.50.230 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Gp5 N-terminal domainCATH (4.3.0)
C2.30.110.50 Mainly Beta Roll Pnp Oxidase Chain ACATH (4.3.0)
C3.55.50.10 Alpha Beta 3-Layer(bab) Sandwich Phage tail protein beta-alpha-beta fold Baseplate protein-like domainsCATH (4.3.0)
C4.10.220.110 Few Secondary Structures Irregular Light-harvesting Protein CATH (4.3.0)
C2.40.50.230 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Gp5 N-terminal domainCATH (4.3.0)
D2.30.110.50 Mainly Beta Roll Pnp Oxidase Chain ACATH (4.3.0)
D3.55.50.10 Alpha Beta 3-Layer(bab) Sandwich Phage tail protein beta-alpha-beta fold Baseplate protein-like domainsCATH (4.3.0)
D4.10.220.110 Few Secondary Structures Irregular Light-harvesting Protein CATH (4.3.0)
D2.40.50.230 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Gp5 N-terminal domainCATH (4.3.0)
E2.30.110.50 Mainly Beta Roll Pnp Oxidase Chain ACATH (4.3.0)
E3.55.50.10 Alpha Beta 3-Layer(bab) Sandwich Phage tail protein beta-alpha-beta fold Baseplate protein-like domainsCATH (4.3.0)
E4.10.220.110 Few Secondary Structures Irregular Light-harvesting Protein CATH (4.3.0)
E2.40.50.230 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Gp5 N-terminal domainCATH (4.3.0)
F2.30.110.50 Mainly Beta Roll Pnp Oxidase Chain ACATH (4.3.0)
F3.55.50.10 Alpha Beta 3-Layer(bab) Sandwich Phage tail protein beta-alpha-beta fold Baseplate protein-like domainsCATH (4.3.0)
F4.10.220.110 Few Secondary Structures Irregular Light-harvesting Protein CATH (4.3.0)
F2.40.50.230 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Gp5 N-terminal domainCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D, E
PF04717Type VI secretion system/phage-baseplate injector OB domain (Phage_base_V)Type VI secretion system/phage-baseplate injector OB domainFamily of bacterial and phage baseplate assembly proteins responsible for forming the small spike at the end of the tail or bacterial pathogenic needle-shaft [1]. This entry represents the OB fold part of the structure. This structure contains an unu ...Domain
A, B, C, D, E
PF22178Bacteriophage T4 gp5 C-terminal trimerisation domain (Gp5_trimer_C)Bacteriophage T4 gp5 C-terminal trimerisation domain- Repeat
A, B, C, D, E
PF05954Phage tail baseplate hub (GPD) (Phage_GPD)Phage tail baseplate hub (GPD)- Family