Research workbench
Crystal structure of the succinyl-diaminopimelate desuccinylase (dape) from acinetobacter baumannii in complex with succinic acid
Analyse Crystal structure of the succinyl-diaminopimelate desuccinylase (dape) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T1Q
- Type
- protein
- Length
- 752 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinyl-diaminopimelate desuccinylase
- EC
- 3.5.1.18
- UniProt
- A3M8H2
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) | protein | 377 | 32% helix, 27% strand | A3M8H2 |
| B | Succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) | protein | 375 | 33% helix, 27% strand | A3M8H2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SIN · Succinic acid · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.68 | 0.96 | 25 | SIN, ACT |
| 2 | 111 | 0.59 | 0.86 | 31 | SIN, ACT |
| 3 | 134 | 0.45 | 0.77 | 28 | empty |
| 4 | 87 | 0.34 | 0.74 | 28 | empty |
| 5 | 56 | 0.28 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2469 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 7T1Q · Crystal Structure of the Succinyl-diaminopimelate Desuccinylase (DapE) from Acinetobacter… · the same entry in another collection · chain A against A, TM-score 1.00
- A3M8H2 · AlphaFold monomer V2.0 prediction for succinyl-diaminopimelate desuccinylase (A3M8H2) · a predicted model of the same protein · chain A against A, TM-score 0.81
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A3M8H2
- Elsewhere: RCSB PDB 7T1Q · PDBe 7T1Q · UniProt A3M8H2
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