PDB ID : 3dbr [ABC]

Color

ARa IRb





 a AR:All Residues
 b IR:Interface Residues

Style





Secondary Structure


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Slab plane

Direction Proportion
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From back %
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Chain
Chain name Ribbon Spacefill Cαonly
OLIGAMI PDB
AE
BF
CK
Title
STRUCTURAL DISSECTION OF A GATING MECHANISM PREVENTING MISACTIVATION OF UBIQUITIN BY NEDD8___sq___S E1 (APPBP1-UBA3ARG190GLN-NEDD8ALA72ARG)

Structure Summary
PDB ID Mutant OPM Pub Med Method/Resolution HETNAM
3dbr
18652489 X-RAY DIFFRACTION/3.05 ZN:ZINC ION
Chain Formula
Amino Acid sequence SCOPe Family Level CATH Homology Level
[ABC] [ABC] [ABC]

Structual Classification
SCOPe
SCOPe ID Chain Class Fold Superfamily Family Protein Domain Species
157482 A:Alpha and beta proteins (a/b)Activating enzymes of the ubiquitin-like proteinsActivating enzymes of the ubiquitin-like proteinsUbiquitin activating enzymes (UBA)Amyloid beta precursor protein-binding protein 1, APPBP1Human (Homo sapiens) [TaxId: 9606]
291508 B:11-11ArtifactsTagsTagsTagsN-terminal TagsSynthetic
239202 B:12-442Alpha and beta proteins (a/b)Activating enzymes of the ubiquitin-like proteinsActivating enzymes of the ubiquitin-like proteinsUbiquitin activating enzymes (UBA)UBA3Human (Homo sapiens) [TaxId: 9606]
157483 C:Alpha and beta proteins (a/b)Activating enzymes of the ubiquitin-like proteinsActivating enzymes of the ubiquitin-like proteinsUbiquitin activating enzymes (UBA)Amyloid beta precursor protein-binding protein 1, APPBP1Human (Homo sapiens) [TaxId: 9606]
291509 D:11-11ArtifactsTagsTagsTagsN-terminal TagsSynthetic
239203 D:12-441Alpha and beta proteins (a/b)Activating enzymes of the ubiquitin-like proteinsActivating enzymes of the ubiquitin-like proteinsUbiquitin activating enzymes (UBA)UBA3Human (Homo sapiens) [TaxId: 9606]
157484 E:Alpha and beta proteins (a/b)Activating enzymes of the ubiquitin-like proteinsActivating enzymes of the ubiquitin-like proteinsUbiquitin activating enzymes (UBA)Amyloid beta precursor protein-binding protein 1, APPBP1Human (Homo sapiens) [TaxId: 9606]
291510 F:11-11ArtifactsTagsTagsTagsN-terminal TagsSynthetic
239204 F:12-441Alpha and beta proteins (a/b)Activating enzymes of the ubiquitin-like proteinsActivating enzymes of the ubiquitin-like proteinsUbiquitin activating enzymes (UBA)UBA3Human (Homo sapiens) [TaxId: 9606]
157485 G:Alpha and beta proteins (a/b)Activating enzymes of the ubiquitin-like proteinsActivating enzymes of the ubiquitin-like proteinsUbiquitin activating enzymes (UBA)Amyloid beta precursor protein-binding protein 1, APPBP1Human (Homo sapiens) [TaxId: 9606]
291511 H:11-11ArtifactsTagsTagsTagsN-terminal TagsSynthetic
239205 H:12-441Alpha and beta proteins (a/b)Activating enzymes of the ubiquitin-like proteinsActivating enzymes of the ubiquitin-like proteinsUbiquitin activating enzymes (UBA)UBA3Human (Homo sapiens) [TaxId: 9606]
291512 I:91-97ArtifactsTagsTagsTagsN-terminal TagsSynthetic
239206 I:99-176Alpha and beta proteins (a+b)beta-Grasp (ubiquitin-like)Ubiquitin-likeUbiquitin-relatedNedd8Human (Homo sapiens) [TaxId: 9606]
291513 J:100-100ArtifactsTagsTagsTagsN-terminal TagsSynthetic
239207 J:101-176Alpha and beta proteins (a+b)beta-Grasp (ubiquitin-like)Ubiquitin-likeUbiquitin-relatedNedd8Human (Homo sapiens) [TaxId: 9606]
291514 K:100-100ArtifactsTagsTagsTagsN-terminal TagsSynthetic
239208 K:101-176Alpha and beta proteins (a+b)beta-Grasp (ubiquitin-like)Ubiquitin-likeUbiquitin-relatedNedd8Human (Homo sapiens) [TaxId: 9606]
239209 L:101-176Alpha and beta proteins (a+b)beta-Grasp (ubiquitin-like)Ubiquitin-likeUbiquitin-relatedNedd8Human (Homo sapiens) [TaxId: 9606]
291515 L:99-100ArtifactsTagsTagsTagsN-terminal TagsSynthetic

CATH
CATH ID Node Class Architecture Topology Homology
3dbrA013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbrB013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbrB021.10.10.520:Orthogonal Bundle:Arc Repressor Mutant, subunit A:Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
3dbrB033.10.20.260:Roll:Ubiquitin-like (UB roll):NEDD8-activating enzyme E1, catalytic subunit
3dbrC013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbrD013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbrD021.10.10.520:Orthogonal Bundle:Arc Repressor Mutant, subunit A:Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
3dbrD033.10.20.260:Roll:Ubiquitin-like (UB roll):NEDD8-activating enzyme E1, catalytic subunit
3dbrE013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbrF013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbrF021.10.10.520:Orthogonal Bundle:Arc Repressor Mutant, subunit A:Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
3dbrF033.10.20.260:Roll:Ubiquitin-like (UB roll):NEDD8-activating enzyme E1, catalytic subunit
3dbrG013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbrH013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbrH021.10.10.520:Orthogonal Bundle:Arc Repressor Mutant, subunit A:Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
3dbrH033.10.20.260:Roll:Ubiquitin-like (UB roll):NEDD8-activating enzyme E1, catalytic subunit
3dbrI003.10.20.90:Roll:Ubiquitin-like (UB roll):Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
3dbrJ003.10.20.90:Roll:Ubiquitin-like (UB roll):Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
3dbrK003.10.20.90:Roll:Ubiquitin-like (UB roll):Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
3dbrL003.10.20.90:Roll:Ubiquitin-like (UB roll):Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1