1DX5

Crystal structure of the thrombin-thrombomodulin complex

External Resource: Annotation


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad1dx5.1 All beta proteins Trypsin-like serine proteases Trypsin-like serine proteases Eukaryotic proteases Thrombin (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Bd1dx5.2 All beta proteins Trypsin-like serine proteases Trypsin-like serine proteases Eukaryotic proteases Thrombin (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Cd1dx5.3 All beta proteins Trypsin-like serine proteases Trypsin-like serine proteases Eukaryotic proteases Thrombin (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Dd1dx5.4 All beta proteins Trypsin-like serine proteases Trypsin-like serine proteases Eukaryotic proteases Thrombin (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
E [auth I]d1dx5i1 Small proteins Knottins (small inhibitors, toxins, lectins) EGF/Laminin EGF-type module Thrombomodulin, different EGF-like domains Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
F [auth J]d1dx5j1 Small proteins Knottins (small inhibitors, toxins, lectins) EGF/Laminin EGF-type module Thrombomodulin, different EGF-like domains Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
G [auth K]d1dx5k1 Small proteins Knottins (small inhibitors, toxins, lectins) EGF/Laminin EGF-type module Thrombomodulin, different EGF-like domains Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
H [auth L]d1dx5l1 Small proteins Knottins (small inhibitors, toxins, lectins) EGF/Laminin EGF-type module Thrombomodulin, different EGF-like domains Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
I [auth M]d1dx5.1 All beta proteins Trypsin-like serine proteases Trypsin-like serine proteases Eukaryotic proteases Thrombin (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
J [auth N]d1dx5.2 All beta proteins Trypsin-like serine proteases Trypsin-like serine proteases Eukaryotic proteases Thrombin (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
K [auth O]d1dx5.3 All beta proteins Trypsin-like serine proteases Trypsin-like serine proteases Eukaryotic proteases Thrombin (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
L [auth P]d1dx5.4 All beta proteins Trypsin-like serine proteases Trypsin-like serine proteases Eukaryotic proteases Thrombin (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
E [auth I]SCOP2 FamilyEGF-type module 8025954 4003198 SCOP2 (2022-06-29)
E [auth I]SCOP2 FamilyEGF-type module 8025955 4003198 SCOP2 (2022-06-29)
E [auth I]SCOP2 FamilyEGF-type module 8025956 4003198 SCOP2 (2022-06-29)
E [auth I]SCOP2 SuperfamilyEGF/Laminin-like 8038333 3000412 SCOP2 (2022-06-29)
E [auth I]SCOP2 SuperfamilyEGF/Laminin-like 8038334 3000412 SCOP2 (2022-06-29)
E [auth I]SCOP2 SuperfamilyEGF/Laminin-like 8038335 3000412 SCOP2 (2022-06-29)
F [auth J]SCOP2B SuperfamilyEGF/Laminin-like 8038335 3000412 SCOP2B (2022-06-29)
F [auth J]SCOP2B SuperfamilyEGF/Laminin-like 8038334 3000412 SCOP2B (2022-06-29)
F [auth J]SCOP2B SuperfamilyEGF/Laminin-like 8038333 3000412 SCOP2B (2022-06-29)
G [auth K]SCOP2B SuperfamilyEGF/Laminin-like 8038333 3000412 SCOP2B (2022-06-29)
G [auth K]SCOP2B SuperfamilyEGF/Laminin-like 8038334 3000412 SCOP2B (2022-06-29)
G [auth K]SCOP2B SuperfamilyEGF/Laminin-like 8038335 3000412 SCOP2B (2022-06-29)
H [auth L]SCOP2B SuperfamilyEGF/Laminin-like 8038335 3000412 SCOP2B (2022-06-29)
H [auth L]SCOP2B SuperfamilyEGF/Laminin-like 8038333 3000412 SCOP2B (2022-06-29)
H [auth L]SCOP2B SuperfamilyEGF/Laminin-like 8038334 3000412 SCOP2B (2022-06-29)
I [auth M]SCOP2B SuperfamilyTrypsin-like serine proteases 8042154 3000114 SCOP2B (2022-06-29)
J [auth N]SCOP2B SuperfamilyTrypsin-like serine proteases 8042154 3000114 SCOP2B (2022-06-29)
K [auth O]SCOP2B SuperfamilyTrypsin-like serine proteases 8042154 3000114 SCOP2B (2022-06-29)
L [auth P]SCOP2B SuperfamilyTrypsin-like serine proteases 8042154 3000114 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
E [auth I]Tme5_EGF_likee1dx5I2 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: Tme5_EGF_likeECOD (1.6)
E [auth I]EGF_CAe1dx5I3 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: EGF_CAECOD (1.6)
F [auth J]Tme5_EGF_likee1dx5J2 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: Tme5_EGF_likeECOD (1.6)
F [auth J]EGF_CAe1dx5J3 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: EGF_CAECOD (1.6)
G [auth K]Tme5_EGF_likee1dx5K2 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: Tme5_EGF_likeECOD (1.6)
G [auth K]EGF_CAe1dx5K3 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: EGF_CAECOD (1.6)
H [auth L]Tme5_EGF_likee1dx5L2 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: Tme5_EGF_likeECOD (1.6)
H [auth L]EGF_CAe1dx5L3 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: EGF_CAECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
E [auth I]2.10.25.10 Mainly Beta Ribbon Laminin LamininCATH (4.3.0)
F [auth J]2.10.25.10 Mainly Beta Ribbon Laminin LamininCATH (4.3.0)
G [auth K]2.10.25.10 Mainly Beta Ribbon Laminin LamininCATH (4.3.0)
H [auth L]2.10.25.10 Mainly Beta Ribbon Laminin LamininCATH (4.3.0)
I [auth M]2.40.10.10 Mainly Beta Beta Barrel Thrombin, subunit H Trypsin-like serine proteasesCATH (4.3.0)
J [auth N]2.40.10.10 Mainly Beta Beta Barrel Thrombin, subunit H Trypsin-like serine proteasesCATH (4.3.0)
K [auth O]2.40.10.10 Mainly Beta Beta Barrel Thrombin, subunit H Trypsin-like serine proteasesCATH (4.3.0)
L [auth P]2.40.10.10 Mainly Beta Beta Barrel Thrombin, subunit H Trypsin-like serine proteasesCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D
PF09396Thrombin light chain (Thrombin_light)Thrombin light chainThrombin is an enzyme that cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII. Prothrombin is activated on the surface of a phospholipid membrane where factor Xa removes the activation peptide and cleave ...Thrombin is an enzyme that cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII. Prothrombin is activated on the surface of a phospholipid membrane where factor Xa removes the activation peptide and cleaves the remaining part into light and heavy chains. This domain corresponds to the light chain of thrombin.
Domain
E [auth I],
F [auth J],
G [auth K],
H [auth L]		PF12662Complement Clr-like EGF-like (cEGF)Complement Clr-like EGF-likecEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL recepto ...cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue.
Domain
I [auth M],
J [auth N],
K [auth O],
L [auth P]		PF00089Trypsin (Trypsin)Trypsin- Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C, D
Thrombin light chain
E [auth I],
F [auth J],
G [auth K],
H [auth L]		Thrombomodulin
I [auth M],
J [auth N],
K [auth O],
L [auth P]		Thrombin heavy chain

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C, D
IPR018992Thrombin light chainDomain
A, B, C, D
IPR037111Thrombin light chain domain superfamilyHomologous Superfamily
A, B, C, D
IPR003966Prothrombin/thrombinFamily
A, B, C, D
IPR018114Serine proteases, trypsin family, histidine active siteActive Site
A, B, C, D
IPR009003Peptidase S1, PA clanHomologous Superfamily
A, B, C, D
IPR033116Serine proteases, trypsin family, serine active siteActive Site
A, B, C, D
IPR001254Serine proteases, trypsin domainDomain
A, B, C, D
IPR035972Gamma-carboxyglutamic acid-rich (GLA) domain superfamilyHomologous Superfamily
A, B, C, D
IPR000001KringleDomain
A, B, C, D
IPR000294Gamma-carboxyglutamic acid-rich (GLA) domainDomain
A, B, C, D
IPR051659Serine Protease S1 Domain-Containing ProteinFamily
A, B, C, D
IPR018056Kringle, conserved siteConserved Site
A, B, C, D
IPR013806Kringle-like foldHomologous Superfamily
A, B, C, D
IPR038178Kringle superfamilyHomologous Superfamily
A, B, C, D
IPR001314Peptidase S1A, chymotrypsin familyFamily
A, B, C, D
IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily
E [auth I],
F [auth J],
G [auth K],
H [auth L]		IPR052126Spindle_Organization_and_ThrombomodulinFamily
E [auth I],
F [auth J],
G [auth K],
H [auth L]		IPR016187C-type lectin foldHomologous Superfamily
E [auth I],
F [auth J],
G [auth K],
H [auth L]		IPR018097EGF-like calcium-binding, conserved siteConserved Site
E [auth I],
F [auth J],
G [auth K],
H [auth L]		IPR026823Complement Clr-like EGF domainDomain
E [auth I],
F [auth J],
G [auth K],
H [auth L]		IPR001304C-type lectin-likeDomain
E [auth I],
F [auth J],
G [auth K],
H [auth L]		IPR016186C-type lectin-like/link domain superfamilyHomologous Superfamily
E [auth I],
F [auth J],
G [auth K],
H [auth L]		IPR000742EGF-like domainDomain
E [auth I],
F [auth J],
G [auth K],
H [auth L]		IPR049883NOTCH1 EGF-like calcium-binding domainDomain
E [auth I],
F [auth J],
G [auth K],
H [auth L]		IPR015149Thrombomodulin-like, EGF-likeDomain
E [auth I],
F [auth J],
G [auth K],
H [auth L]		IPR009030Growth factor receptor cysteine-rich domain superfamilyHomologous Superfamily
E [auth I],
F [auth J],
G [auth K],
H [auth L]		IPR001881EGF-like calcium-binding domainDomain
E [auth I],
F [auth J],
G [auth K],
H [auth L]		IPR000152EGF-type aspartate/asparagine hydroxylation sitePTM
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR018992Thrombin light chainDomain
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR037111Thrombin light chain domain superfamilyHomologous Superfamily
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR003966Prothrombin/thrombinFamily
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR018114Serine proteases, trypsin family, histidine active siteActive Site
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR009003Peptidase S1, PA clanHomologous Superfamily
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR033116Serine proteases, trypsin family, serine active siteActive Site
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR001254Serine proteases, trypsin domainDomain
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR035972Gamma-carboxyglutamic acid-rich (GLA) domain superfamilyHomologous Superfamily
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR000001KringleDomain
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR000294Gamma-carboxyglutamic acid-rich (GLA) domainDomain
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR051659Serine Protease S1 Domain-Containing ProteinFamily
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR018056Kringle, conserved siteConserved Site
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR013806Kringle-like foldHomologous Superfamily
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR038178Kringle superfamilyHomologous Superfamily
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR001314Peptidase S1A, chymotrypsin familyFamily
I [auth M],
J [auth N],
K [auth O],
L [auth P]		IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A, B, C, D
Pharos:  P00734
E [auth I],
F [auth J],
G [auth K],
H [auth L]		Pharos:  P07204
I [auth M],
J [auth N],
K [auth O],
L [auth P]		Pharos:  P00734