MolNFT v1 · #177239 · protein
Crystal structure of D-succinylase (dsa) from cupriavidus sp. P4-10-C
7EBY: “Crystal structure of D-succinylase (dsa) from cupriavidus sp. P4-10-C”. X-ray diffraction, 2 ligands (CA, CO3), 20 pockets (best druggability 0.77). MolNFT v1 #177239 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7EBY
- Type
- protein
- Length
- 4,569 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-succinylase
- UniProt
- A0A0N7KZ58
- Ligands
- CA, CO3
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | D-succinylase | protein | 761 | 38% helix, 22% strand | A0A0N7KZ58 |
| C, D, E | D-succinylase | protein | 762 | 38% helix, 22% strand | A0A0N7KZ58 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
- CO3 · Carbonate ion · ion · 18 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 21 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.77 | 0.81 | 93 | GOL |
| 2 | 1107 | 0.77 | 0.79 | 124 | GOL |
| 3 | 1085 | 0.74 | 0.77 | 85 | CO3 |
| 4 | 1074 | 0.74 | 0.77 | 94 | CO3 |
| 5 | 1109 | 0.74 | 0.77 | 86 | GOL, CO3 |
Interfaces
8 interfaces between chains.
- A–B · 1322 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1302 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1301 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 450 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 395 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7EBY · Crystal structure of 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 7EBY · PDBe 7EBY · UniProt A0A0N7KZ58
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