MolNFT v1 · #59972 · protein
Crystal structure of SUCCINYLGLUTAMATEDESUCCINYLASE/ASPARTOACYLASE from rhodobacter sphaeroides
3CDX: “Crystal structure of SUCCINYLGLUTAMATEDESUCCINYLASE/ASPARTOACYLASE from rhodobacter sphaeroides”. X-ray diffraction, 1 ligand (CA), 14 pockets (best druggability 0.80). MolNFT v1 #59972 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3CDX
- Type
- protein
- Length
- 1,958 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SUCCINYLGLUTAMATEDESUCCINYLASE/ASPARTOACYLASE
- UniProt
- Q3HKK3
- Ligands
- CA
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SUCCINYLGLUTAMATEDESUCCINYLASE/ASPARTOACYLASE | protein | 329 | 25% helix, 30% strand | Q3HKK3 |
| B | SUCCINYLGLUTAMATEDESUCCINYLASE/ASPARTOACYLASE | protein | 328 | 25% helix, 30% strand | Q3HKK3 |
| C | SUCCINYLGLUTAMATEDESUCCINYLASE/ASPARTOACYLASE | protein | 325 | 25% helix, 31% strand | Q3HKK3 |
| D | SUCCINYLGLUTAMATEDESUCCINYLASE/ASPARTOACYLASE | protein | 322 | 25% helix, 32% strand | Q3HKK3 |
| E | SUCCINYLGLUTAMATEDESUCCINYLASE/ASPARTOACYLASE | protein | 326 | 25% helix, 32% strand | Q3HKK3 |
| F | SUCCINYLGLUTAMATEDESUCCINYLASE/ASPARTOACYLASE | protein | 328 | 25% helix, 30% strand | Q3HKK3 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.80 | 0.82 | 113 | CA |
| 2 | 850 | 0.78 | 0.81 | 98 | empty |
| 3 | 489 | 0.74 | 0.83 | 63 | CA |
| 4 | 960 | 0.74 | 0.77 | 86 | empty |
| 5 | 772 | 0.70 | 0.77 | 53 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1892 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1888 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1887 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 901 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 890 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3CDX · Crystal structure of succinylglutamatedesuccinylase/aspartoacylase from Rhodobacter… · 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 Q3HKK3
- Elsewhere: RCSB PDB 3CDX · PDBe 3CDX · UniProt Q3HKK3
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