MolNFT v1 · #137023 · protein
Crystal structure of succinate semialdehyde dehydrogenase from burkholderia vietnamiensis
5VBF · NAD-dependent succinate-semialdehyde dehydrogenase: “Crystal structure of succinate semialdehyde dehydrogenase from burkholderia vietnamiensis”. X-ray diffraction, 1 ligand (UNX), 20 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 5VBF
- Type
- protein
- Length
- 3,815 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent succinate-semialdehyde dehydrogenase
- UniProt
- A0A132DEP7
- Ligands
- UNX
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD-dependent succinate-semialdehyde dehydrogenase | protein | 478 | 42% helix, 23% strand | A0A132DEP7 |
| C, E, F | NAD-dependent succinate-semialdehyde dehydrogenase | protein | 476 | 42% helix, 23% strand | A0A132DEP7 |
| D, G, H | NAD-dependent succinate-semialdehyde dehydrogenase | protein | 477 | 42% helix, 23% strand | A0A132DEP7 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, F, G, H
- FMT · Formic acid · additive · 4 copies · chains A, B, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.87 | 0.90 | 93 | empty |
| 2 | 629 | 0.87 | 0.92 | 90 | GOL |
| 3 | 188 | 0.84 | 0.98 | 27 | empty |
| 4 | 305 | 0.82 | 0.93 | 57 | empty |
| 5 | 172 | 0.82 | 0.97 | 25 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2558 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 2557 Ų buried · 37 hydrogen bonds · protein-protein
- G–H · 2557 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2535 Ų buried · 37 hydrogen bonds · protein-protein
- E–H · 1078 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5VBF · Crystal structure of succinate semialdehyde dehydrogenase from Burkholderia vietnamiensis · the same entry in another collection · chain C against C, 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 A0A132DEP7
- Elsewhere: RCSB PDB 5VBF · PDBe 5VBF · UniProt A0A132DEP7
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