5NRI
Crystal structure of Burkholderia pseudomallei D-alanine-D-alanine ligase in complex with AMP and D-Ala-D-Ala
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
B | d5nrib1 | Alpha and beta proteins (a/b) | PreATP-grasp domain | PreATP-grasp domain | automated matches | automated matches | (Burkholderia pseudomallei 1106a ) [TaxId: 357348 ], | SCOPe (2.08) |
B | d5nrib2 | Alpha and beta proteins (a+b) | ATP-grasp | Glutathione synthetase ATP-binding domain-like | automated matches | automated matches | (Burkholderia pseudomallei 1106a ) [TaxId: 357348 ], | SCOPe (2.08) |
A | d5nria1 | Alpha and beta proteins (a/b) | PreATP-grasp domain | PreATP-grasp domain | automated matches | automated matches | (Burkholderia pseudomallei 1106a ) [TaxId: 357348 ], | SCOPe (2.08) |
A | d5nria2 | Alpha and beta proteins (a+b) | ATP-grasp | Glutathione synthetase ATP-binding domain-like | automated matches | automated matches | (Burkholderia pseudomallei 1106a ) [TaxId: 357348 ], | SCOPe (2.08) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
B | ATP-grasp | e5nriB2 | A: a+b complex topology | X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology) | H: Protein kinase/SAICAR synthase/ATP-grasp | T: ATP-grasp | F: ATP-grasp | ECOD (1.6) |
B | Dala_Dala_lig_N | e5nriB1 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: PreATP-grasp domain | F: Dala_Dala_lig_N | ECOD (1.6) |
A | ATP-grasp | e5nriA2 | A: a+b complex topology | X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology) | H: Protein kinase/SAICAR synthase/ATP-grasp | T: ATP-grasp | F: ATP-grasp | ECOD (1.6) |
A | Dala_Dala_lig_N | e5nriA1 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: PreATP-grasp domain | F: Dala_Dala_lig_N | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
B | 3.40.50.20 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | CATH (utative) | |
B | 3.30.1490.20 | Alpha Beta | 2-Layer Sandwich | Dna Ligase | domain 1 | CATH (utative) |
A | 3.40.50.20 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | CATH (utative) | |
A | 3.30.1490.20 | Alpha Beta | 2-Layer Sandwich | Dna Ligase | domain 1 | CATH (utative) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF07478 | D-ala D-ala ligase C-terminus (Dala_Dala_lig_C) | D-ala D-ala ligase C-terminus | - | Family | |
PF01820 | D-ala D-ala ligase N-terminus (Dala_Dala_lig_N) | D-ala D-ala ligase N-terminus | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR011761 | ATP-grasp fold | Domain | |
IPR011095 | D-alanine--D-alanine ligase, C-terminal | Domain | |
IPR013815 | ATP-grasp fold, subdomain 1 | Homologous Superfamily | |
IPR000291 | D-alanine--D-alanine ligase/VANA/B/C, conserved site | Conserved Site | |
IPR016185 | Pre-ATP-grasp domain superfamily | Homologous Superfamily | |
IPR005905 | D-alanine--D-alanine ligase | Family | |
IPR011127 | D-alanine--D-alanine ligase, N-terminal domain | Domain |