Research workbench
Crystal structure of spermidine N-acetyltransferase from vibrio cholerae in complex with CoA and spermine
Analyse Crystal structure of spermidine N-acetyltransferase from vibrio cholerae in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R87
- Type
- protein
- Length
- 2,031 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine N1-acetyltransferase
- UniProt
- Q9KL03
- Ligands
- COA, SPM
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G, K | Spermidine N1-acetyltransferase | protein | 170 | 35% helix, 32% strand | Q9KL03 |
| B, C, F, H, I, J, L | Spermidine N1-acetyltransferase | protein | 169 | 31% helix, 35% strand | Q9KL03 |
| D | Spermidine N1-acetyltransferase | protein | 168 | 30% helix, 35% strand | Q9KL03 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SPM · Spermine · ligand · 6 copies · chains E, G, H, I, J, L, K
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains F, H, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.85 | 0.86 | 128 | COA, SPM |
| 2 | 825 | 0.83 | 0.85 | 111 | empty |
| 3 | 985 | 0.82 | 0.83 | 94 | SPM, COA |
| 4 | 898 | 0.81 | 0.83 | 97 | COA, SPM |
| 5 | 790 | 0.80 | 0.83 | 93 | COA, SPM |
Interfaces
23 interfaces between chains.
- K–L · 1021 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1020 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1016 Ų buried · 26 hydrogen bonds · protein-protein
- I–J · 1005 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 997 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4R87 · Crystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with… · the same entry in another collection · chain L against L, 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 Q9KL03
- Elsewhere: RCSB PDB 4R87 · PDBe 4R87 · UniProt Q9KL03
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