PDB ID : 3dbh [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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Chain
Chain name Ribbon Spacefill Cαonly
OLIGAMI PDB
AC
BD
CJ
Title
STRUCTURAL DISSECTION OF A GATING MECHANISM PREVENTING MISACTIVATION OF UBIQUITIN BY NEDD8___sq___S E1 (APPBP1-UBA3ARG190ALA-NEDD8ALA72ARG)

Structure Summary
PDB ID Mutant OPM Pub Med Method/Resolution HETNAM
3dbh
18652489 X-RAY DIFFRACTION/2.85 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
157468 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]
291498 B:11-11ArtifactsTagsTagsTagsN-terminal TagsSynthetic
161640 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]
157469 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]
291499 D:11-11ArtifactsTagsTagsTagsN-terminal TagsSynthetic
161641 D: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]
157470 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]
291500 F:11-11ArtifactsTagsTagsTagsN-terminal TagsSynthetic
161642 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]
157471 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]
291501 H:11-11ArtifactsTagsTagsTagsN-terminal TagsSynthetic
161643 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]
157472 I:101-176Alpha and beta proteins (a+b)beta-Grasp (ubiquitin-like)Ubiquitin-likeUbiquitin-relatedNedd8Human (Homo sapiens) [TaxId: 9606]
291502 I:91-100ArtifactsTagsTagsTagsN-terminal TagsSynthetic
161644 J:Alpha and beta proteins (a+b)beta-Grasp (ubiquitin-like)Ubiquitin-likeUbiquitin-relatedNedd8Human (Homo sapiens) [TaxId: 9606]
161645 K:Alpha and beta proteins (a+b)beta-Grasp (ubiquitin-like)Ubiquitin-likeUbiquitin-relatedNedd8Human (Homo sapiens) [TaxId: 9606]
161646 L:Alpha and beta proteins (a+b)beta-Grasp (ubiquitin-like)Ubiquitin-likeUbiquitin-relatedNedd8Human (Homo sapiens) [TaxId: 9606]

CATH
CATH ID Node Class Architecture Topology Homology
3dbhA013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbhB013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbhB021.10.10.520:Orthogonal Bundle:Arc Repressor Mutant, subunit A:Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
3dbhB033.10.20.260:Roll:Ubiquitin-like (UB roll):NEDD8-activating enzyme E1, catalytic subunit
3dbhC013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbhD013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbhD021.10.10.520:Orthogonal Bundle:Arc Repressor Mutant, subunit A:Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
3dbhD033.10.20.260:Roll:Ubiquitin-like (UB roll):NEDD8-activating enzyme E1, catalytic subunit
3dbhE013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbhF013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbhF021.10.10.520:Orthogonal Bundle:Arc Repressor Mutant, subunit A:Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
3dbhF033.10.20.260:Roll:Ubiquitin-like (UB roll):NEDD8-activating enzyme E1, catalytic subunit
3dbhG013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbhH013.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3dbhH021.10.10.520:Orthogonal Bundle:Arc Repressor Mutant, subunit A:Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
3dbhH033.10.20.260:Roll:Ubiquitin-like (UB roll):NEDD8-activating enzyme E1, catalytic subunit
3dbhI003.10.20.90:Roll:Ubiquitin-like (UB roll):Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
3dbhJ003.10.20.90:Roll:Ubiquitin-like (UB roll):Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
3dbhK003.10.20.90:Roll:Ubiquitin-like (UB roll):Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
3dbhL003.10.20.90:Roll:Ubiquitin-like (UB roll):Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1