MolNFT v1 · #177180 · protein
Crystal structure of L182E D-succinylase (dsa) from cupriavidus sp. P4-10-C
7EA4: “Crystal structure of L182E D-succinylase (dsa) from cupriavidus sp. P4-10-C”. X-ray diffraction, 4 ligands (CAD, CA, CL), 18 pockets (best druggability 0.74). MolNFT v1 #177180 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7EA4
- Type
- protein
- Length
- 1,523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-succinylase
- UniProt
- A0A0N7KZ58
- Ligands
- CAD, CA, CL, CO3
- Pockets
- 18 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-succinylase | protein | 762 | 38% helix, 21% strand | A0A0N7KZ58 |
| B | D-succinylase | protein | 761 | 38% helix, 21% strand | A0A0N7KZ58 |
Ligands and binding sites
- CAD · Cacodylic acid · ligand · 2 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- CO3 · Carbonate ion · ion · chains A
- SIN · Succinic acid · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.74 | 0.77 | 86 | CAD, GOL, SIN |
| 2 | 1092 | 0.74 | 0.77 | 83 | SIN |
| 3 | 408 | 0.73 | 0.84 | 42 | empty |
| 4 | 936 | 0.71 | 0.75 | 77 | empty |
| 5 | 62 | 0.64 | 0.93 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1442 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7EA4 · Crystal Structure of L182E D-Succinylase (DSA) from Cupriavidus sp. P4-10-C · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0N7KZ58
- Elsewhere: RCSB PDB 7EA4 · PDBe 7EA4 · UniProt A0A0N7KZ58
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