3KTM

Structure of the Heparin-induced E1-Dimer of the Amyloid Precursor Protein (APP)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyAmyloid beta a4 protein copper binding domain (domain 2) 8041099 3000618 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyA heparin-binding domain 8037154 3001388 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyAmyloid beta a4 protein copper binding domain (domain 2) 8041099 3000618 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyA heparin-binding domain 8037154 3001388 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyA heparin-binding domain 8037154 3001388 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyAmyloid beta a4 protein copper binding domain (domain 2) 8041099 3000618 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyAmyloid beta a4 protein copper binding domain (domain 2) 8041099 3000618 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyA heparin-binding domain 8037154 3001388 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyAmyloid beta a4 protein copper binding domain (domain 2) 8041099 3000618 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyA heparin-binding domain 8037154 3001388 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyA heparin-binding domain 8037154 3001388 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyAmyloid beta a4 protein copper binding domain (domain 2) 8041099 3000618 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyA heparin-binding domain 8037154 3001388 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyAmyloid beta a4 protein copper binding domain (domain 2) 8041099 3000618 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyAmyloid beta a4 protein copper binding domain (domain 2) 8041099 3000618 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyA heparin-binding domain 8037154 3001388 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AAPP_Cu_bde3ktmA2 A: a+b two layersX: Dodecin subunit-likeH: Amyloid beta a4 protein copper binding domain (domain 2) (From Topology)T: Amyloid beta a4 protein copper binding domain (domain 2)F: APP_Cu_bdECOD (1.6)
AAPP_Ne3ktmA1 A: a+b complex topologyX: SRCR-likeH: A heparin-binding domain (From Topology)T: A heparin-binding domainF: APP_NECOD (1.6)
BAPP_Cu_bde3ktmB1 A: a+b two layersX: Dodecin subunit-likeH: Amyloid beta a4 protein copper binding domain (domain 2) (From Topology)T: Amyloid beta a4 protein copper binding domain (domain 2)F: APP_Cu_bdECOD (1.6)
BAPP_Ne3ktmB2 A: a+b complex topologyX: SRCR-likeH: A heparin-binding domain (From Topology)T: A heparin-binding domainF: APP_NECOD (1.6)
CAPP_Cu_bde3ktmC1 A: a+b two layersX: Dodecin subunit-likeH: Amyloid beta a4 protein copper binding domain (domain 2) (From Topology)T: Amyloid beta a4 protein copper binding domain (domain 2)F: APP_Cu_bdECOD (1.6)
CAPP_Ne3ktmC2 A: a+b complex topologyX: SRCR-likeH: A heparin-binding domain (From Topology)T: A heparin-binding domainF: APP_NECOD (1.6)
DAPP_Cu_bde3ktmD1 A: a+b two layersX: Dodecin subunit-likeH: Amyloid beta a4 protein copper binding domain (domain 2) (From Topology)T: Amyloid beta a4 protein copper binding domain (domain 2)F: APP_Cu_bdECOD (1.6)
DAPP_Ne3ktmD2 A: a+b complex topologyX: SRCR-likeH: A heparin-binding domain (From Topology)T: A heparin-binding domainF: APP_NECOD (1.6)
EAPP_Cu_bde3ktmE1 A: a+b two layersX: Dodecin subunit-likeH: Amyloid beta a4 protein copper binding domain (domain 2) (From Topology)T: Amyloid beta a4 protein copper binding domain (domain 2)F: APP_Cu_bdECOD (1.6)
EAPP_Ne3ktmE2 A: a+b complex topologyX: SRCR-likeH: A heparin-binding domain (From Topology)T: A heparin-binding domainF: APP_NECOD (1.6)
FAPP_Cu_bde3ktmF1 A: a+b two layersX: Dodecin subunit-likeH: Amyloid beta a4 protein copper binding domain (domain 2) (From Topology)T: Amyloid beta a4 protein copper binding domain (domain 2)F: APP_Cu_bdECOD (1.6)
FAPP_Ne3ktmF2 A: a+b complex topologyX: SRCR-likeH: A heparin-binding domain (From Topology)T: A heparin-binding domainF: APP_NECOD (1.6)
GAPP_Cu_bde3ktmG1 A: a+b two layersX: Dodecin subunit-likeH: Amyloid beta a4 protein copper binding domain (domain 2) (From Topology)T: Amyloid beta a4 protein copper binding domain (domain 2)F: APP_Cu_bdECOD (1.6)
GAPP_Ne3ktmG2 A: a+b complex topologyX: SRCR-likeH: A heparin-binding domain (From Topology)T: A heparin-binding domainF: APP_NECOD (1.6)
HAPP_Cu_bde3ktmH1 A: a+b two layersX: Dodecin subunit-likeH: Amyloid beta a4 protein copper binding domain (domain 2) (From Topology)T: Amyloid beta a4 protein copper binding domain (domain 2)F: APP_Cu_bdECOD (1.6)
HAPP_Ne3ktmH2 A: a+b complex topologyX: SRCR-likeH: A heparin-binding domain (From Topology)T: A heparin-binding domainF: APP_NECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.90.570.10 Alpha Beta Alpha-Beta Complex Sugar Binding Protein, Amyloid A4 Protein Chain ACATH (4.3.0)
A3.30.1490.140 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1CATH (4.3.0)
B3.90.570.10 Alpha Beta Alpha-Beta Complex Sugar Binding Protein, Amyloid A4 Protein Chain ACATH (4.3.0)
B3.30.1490.140 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1CATH (4.3.0)
C3.90.570.10 Alpha Beta Alpha-Beta Complex Sugar Binding Protein, Amyloid A4 Protein Chain ACATH (4.3.0)
C3.30.1490.140 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1CATH (4.3.0)
D3.90.570.10 Alpha Beta Alpha-Beta Complex Sugar Binding Protein, Amyloid A4 Protein Chain ACATH (4.3.0)
D3.30.1490.140 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1CATH (4.3.0)
E3.90.570.10 Alpha Beta Alpha-Beta Complex Sugar Binding Protein, Amyloid A4 Protein Chain ACATH (4.3.0)
E3.30.1490.140 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1CATH (4.3.0)
F3.90.570.10 Alpha Beta Alpha-Beta Complex Sugar Binding Protein, Amyloid A4 Protein Chain ACATH (4.3.0)
F3.30.1490.140 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1CATH (4.3.0)
G3.90.570.10 Alpha Beta Alpha-Beta Complex Sugar Binding Protein, Amyloid A4 Protein Chain ACATH (4.3.0)
G3.30.1490.140 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1CATH (4.3.0)
H3.90.570.10 Alpha Beta Alpha-Beta Complex Sugar Binding Protein, Amyloid A4 Protein Chain ACATH (4.3.0)
H3.30.1490.140 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D, E
PF02177Amyloid A4 N-terminal heparin-binding (APP_N)Amyloid A4 N-terminal heparin-bindingThis N-terminal domain of APP, amyloid precursor protein, is the heparin-binding domain of the protein. this region is also responsible for stimulation of neurite outgrowth. The structure reveals both a highly charged basic surface that may interact ...This N-terminal domain of APP, amyloid precursor protein, is the heparin-binding domain of the protein. this region is also responsible for stimulation of neurite outgrowth. The structure reveals both a highly charged basic surface that may interact with glycosaminoglycans in the brain and an abutting hydrophobic surface that is proposed to play an important functional role such as in dimerisation or ligand-binding. Structural similarities with cysteine-rich growth factors, taken together with its known growth-promoting properties, suggest the APP N-terminal domain could function as a growth factor in vivo [1].
Domain
A, B, C, D, E
PF12924Copper-binding of amyloid precursor, CuBD (APP_Cu_bd)Copper-binding of amyloid precursor, CuBDThis short domain, part of the extra-cellular N-terminus of the amyloid precursor protein, APP, can bind both copper and zinc, CuBD. The structure of Cu2+-bound CuBD reveals that the metal ligands are His147, His151, Tyr168 and two water molecules, ...This short domain, part of the extra-cellular N-terminus of the amyloid precursor protein, APP, can bind both copper and zinc, CuBD. The structure of Cu2+-bound CuBD reveals that the metal ligands are His147, His151, Tyr168 and two water molecules, which are arranged in a square pyramidal geometry. The structure of Cu+-bound CuBD is almost identical to the Cu2+-bound structure except for the loss of one of the water ligands. The geometry of the site is unfavourable for Cu+, thus providing a mechanism by which CuBD could readily transfer Cu ions to other proteins.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C, D, E
Amyloid beta A4 protein

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C, D, E
IPR013803Amyloidogenic glycoprotein, amyloid-beta peptideDomain
A, B, C, D, E
IPR008154Amyloidogenic glycoprotein, extracellularDomain
A, B, C, D, E
IPR036176E2 domain superfamilyHomologous Superfamily
A, B, C, D, E
IPR024329Amyloidogenic glycoprotein, E2 domainDomain
A, B, C, D, E
IPR036669Amyloidogenic glycoprotein, copper-binding domain superfamilyHomologous Superfamily
A, B, C, D, E
IPR019745Amyloidogenic glycoprotein, intracellular domain, conserved siteConserved Site
A, B, C, D, E
IPR011178Amyloidogenic glycoprotein, copper-bindingDomain
A, B, C, D, E
IPR037071Amyloidogenic glycoprotein, amyloid-beta peptide superfamilyHomologous Superfamily
A, B, C, D, E
IPR020901Proteinase inhibitor I2, Kunitz, conserved siteConserved Site
A, B, C, D, E
IPR019744Amyloidogenic glycoprotein, copper-binding domain conserved siteConserved Site
A, B, C, D, E
IPR002223Pancreatic trypsin inhibitor Kunitz domainDomain
A, B, C, D, E
IPR015849Amyloidogenic glycoprotein, heparin-bindingDomain
A, B, C, D, E
IPR036454Amyloidogenic glycoprotein, heparin-binding domain superfamilyHomologous Superfamily
A, B, C, D, E
IPR011993PH-like domain superfamilyHomologous Superfamily
A, B, C, D, E
IPR019543Beta-amyloid precursor protein C-terminalDomain
A, B, C, D, E
IPR036880Pancreatic trypsin inhibitor Kunitz domain superfamilyHomologous Superfamily
A, B, C, D, E
IPR008155Amyloidogenic glycoproteinFamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A, B, C, D, E
PharosP05067