MolNFT v1 · #146210 · protein
Crystal structure of E33Q and E41Q mutant forms of the SPERMIDINE/SPERMINE N-acetyltransferase speg from vibrio cholerae
6DAU · Spermidine N1-acetyltransferase: “Crystal structure of E33Q and E41Q mutant forms of the SPERMIDINE/SPERMINE N-acetyltransferase speg from…”. X-ray diffraction, 12 pockets (best druggability 0.85). MolNFT v1 #146210 on GenesisL1: 3D…
- PDB
- 6DAU
- Type
- protein
- Length
- 1,014 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine N1-acetyltransferase
- EC
- 2.3.1.57
- UniProt
- A0A2L2MBX3
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine N1-acetyltransferase (EC 2.3.1.57) | protein | 170 | 33% helix, 38% strand | A0A2L2MBX3 |
| B | Spermidine N1-acetyltransferase (EC 2.3.1.57) | protein | 168 | 33% helix, 39% strand | A0A2L2MBX3 |
| C | Spermidine N1-acetyltransferase (EC 2.3.1.57) | protein | 172 | 32% helix, 38% strand | A0A2L2MBX3 |
| D | Spermidine N1-acetyltransferase (EC 2.3.1.57) | protein | 171 | 31% helix, 38% strand | A0A2L2MBX3 |
| E | Spermidine N1-acetyltransferase (EC 2.3.1.57) | protein | 166 | 33% helix, 39% strand | A0A2L2MBX3 |
| F | Spermidine N1-acetyltransferase (EC 2.3.1.57) | protein | 167 | 31% helix, 38% strand | A0A2L2MBX3 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.85 | 0.89 | 81 | empty |
| 2 | 775 | 0.85 | 0.87 | 88 | empty |
| 3 | 1184 | 0.79 | 0.81 | 90 | empty |
| 4 | 96 | 0.76 | 0.97 | 22 | empty |
| 5 | 1055 | 0.75 | 0.78 | 85 | empty |
Interfaces
9 interfaces between chains.
- A–C · 1155 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1136 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 745 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 701 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 563 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6DAU · Crystal structure of E33Q and E41Q mutant forms of the spermidine/spermine… · 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 A0A2L2MBX3
- Elsewhere: RCSB PDB 6DAU · PDBe 6DAU · UniProt A0A2L2MBX3
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