3B13 | pdb_00003b13

Crystal structure of the DHR-2 domain of DOCK2 in complex with Rac1 (T17N mutant)

External Resource: Annotation


Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Dd3b13d_ Alpha and beta proteins (a/b) P-loop containing nucleoside triphosphate hydrolases P-loop containing nucleoside triphosphate hydrolases G proteins Rac human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Bd3b13b_ Alpha and beta proteins (a/b) P-loop containing nucleoside triphosphate hydrolases P-loop containing nucleoside triphosphate hydrolases G proteins Rac human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
DSCOP2B SuperfamilyRas-like P-loop GTPases 8057406 3002022 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyRas-like P-loop GTPases 8057406 3002022 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
DRase3b13D2 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: RasECOD (1.6)
BRase3b13B1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: RasECOD (1.6)
CDHR-2_1st_1e3b13C6 A: alpha superhelicesX: Repetitive alpha hairpinsH: Helical domain in dedicator of cytokinesis protein 9 (From Topology)T: Helical domain in dedicator of cytokinesis protein 9F: DHR-2_1st_1ECOD (1.6)
CDHR-2_3rde3b13C5 A: alpha superhelicesX: Repetitive alpha hairpinsH: Helical domain in dedicator of cytokinesis protein 9 (From Topology)T: Helical domain in dedicator of cytokinesis protein 9F: DHR-2_3rdECOD (1.6)
CDHR-2_2nde3b13C4 A: a+b two layersX: Barrel domain in dedicator of cytokinesis protein 9 (From Topology)H: Barrel domain in dedicator of cytokinesis protein 9 (From Topology)T: Barrel domain in dedicator of cytokinesis protein 9F: DHR-2_2ndECOD (1.6)
ADHR-2_1st_1e3b13A3 A: alpha superhelicesX: Repetitive alpha hairpinsH: Helical domain in dedicator of cytokinesis protein 9 (From Topology)T: Helical domain in dedicator of cytokinesis protein 9F: DHR-2_1st_1ECOD (1.6)
ADHR-2_3rde3b13A2 A: alpha superhelicesX: Repetitive alpha hairpinsH: Helical domain in dedicator of cytokinesis protein 9 (From Topology)T: Helical domain in dedicator of cytokinesis protein 9F: DHR-2_3rdECOD (1.6)
ADHR-2_2nde3b13A1 A: a+b two layersX: Barrel domain in dedicator of cytokinesis protein 9 (From Topology)H: Barrel domain in dedicator of cytokinesis protein 9 (From Topology)T: Barrel domain in dedicator of cytokinesis protein 9F: DHR-2_2ndECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
D3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)
B3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (4.3.0)
C1.25.40.410 Mainly Alpha Alpha Horseshoe Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat DOCK DHR2 domain, lobe ACATH (4.3.0)
C1.20.58.740 Mainly Alpha Up-down Bundle Methane Monooxygenase Hydroxylase Chain G, domain 1CATH (4.3.0)
A1.25.40.410 Mainly Alpha Alpha Horseshoe Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat DOCK DHR2 domain, lobe ACATH (4.3.0)
A1.20.58.740 Mainly Alpha Up-down Bundle Methane Monooxygenase Hydroxylase Chain G, domain 1CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
B, D
PF00071Ras family (Ras)Ras familyIncludes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motili ...Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].
Domain
A, C
PF20421DHR-2, Lobe C (DHR-2_Lobe_C)DHR-2, Lobe C- Repeat
A, C
PF06920DHR-2, Lobe A (DHR-2_Lobe_A)DHR-2, Lobe A- Repeat
A, C
PF20422DHR-2, Lobe B (DHR-2_Lobe_B)DHR-2, Lobe BDOCK (dedicator of cytokinesis) proteins are guanine nucleotide exchange factors (GEFs) that activate some small GTPases, such as Rac or Cdc42, by exchanging bound GDP for free GTP to control cell migration, morphogenesis, and phagocytosis. These pro ...DOCK (dedicator of cytokinesis) proteins are guanine nucleotide exchange factors (GEFs) that activate some small GTPases, such as Rac or Cdc42, by exchanging bound GDP for free GTP to control cell migration, morphogenesis, and phagocytosis. These proteins share a DOCK-type C2 domain (also termed the DOCK-homology region (DHR)-1) at the N-terminal, and the DHR-2 domain (also termed the DOCKER domain) at the C-terminal. DHR-2 is the GEF catalytic domain organised into three lobes A, B and C, with the Rho-family binding site and catalytic centre generated entirely from lobes B and C. This entry represents Lobe B which adopts an unusual architecture of two antiparallel beta sheets disposed in a loosely packed orthogonal arrangement. This lobe changes its position relative to lobe C and the bound GTPase, which suggests that lobe B distinguishes between the switch 1 conformations of Rac1 and Cdc42 [2].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
B, D
Ras-related C3 botulinum toxin substrate 1
A, C
Dedicator of cytokinesis protein 2

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
B, D
IPR001806Small GTPaseFamily
B, D
IPR003578Small GTPase RhoFamily
B, D
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
B, D
IPR005225Small GTP-binding domainDomain
A, C
IPR043162Dedicator of cytokinesis, C-terminal, lobe CHomologous Superfamily
A, C
IPR016024Armadillo-type foldHomologous Superfamily
A, C
IPR042455Dedicator of cytokinesis, N-terminal, subdomain 1Homologous Superfamily
A, C
IPR026791Dedicator of cytokinesisFamily
A, C
IPR046773DOCKER, Lobe CDomain
A, C
IPR036028SH3-like domain superfamilyHomologous Superfamily
A, C
IPR056372Dedicator of cytokinesis, TPR repeats regionDomain
A, C
IPR046770DOCKER, Lobe BDomain
A, C
IPR027357DOCKER domainDomain
A, C
IPR046769DOCKER, Lobe ADomain
A, C
IPR032376Dedicator of cytokinesis, N-terminal domainDomain
A, C
IPR026799Dedicator of cytokinesis protein 2, DHR2 domainDomain
A, C
IPR001452SH3 domainDomain
A, C
IPR035892C2 domain superfamilyHomologous Superfamily
A, C
IPR027007C2 DOCK-type domainDomain
A, C
IPR043161Dedicator of cytokinesis, C-terminal, lobe AHomologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
B, D
Pharos:  P63000
A, C
Pharos:  Q92608