Research workbench
Crystal structure of serine acetyltransferase cyse from yersinia pestis
Analyse Crystal structure of serine acetyltransferase cyse from yersinia pestis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GVD
- Type
- protein
- Length
- 3,162 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine acetyltransferase
- EC
- 2.3.1.30
- UniProt
- Q0WKM4
- Ligands
- CYS, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 9 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine acetyltransferase (EC 2.3.1.30) | protein | 271 | 45% helix, 14% strand | Q0WKM4 |
| B | Serine acetyltransferase (EC 2.3.1.30) | protein | 265 | 44% helix, 15% strand | Q0WKM4 |
| C | Serine acetyltransferase (EC 2.3.1.30) | protein | 262 | 45% helix, 15% strand | Q0WKM4 |
| D | Serine acetyltransferase (EC 2.3.1.30) | protein | 262 | 43% helix, 15% strand | Q0WKM4 |
| E, G | Serine acetyltransferase (EC 2.3.1.30) | protein | 263 | 44% helix, 14% strand | Q0WKM4 |
| F, J, L | Serine acetyltransferase (EC 2.3.1.30) | protein | 261 | 43% helix, 15% strand | Q0WKM4 |
| H | Serine acetyltransferase (EC 2.3.1.30) | protein | 261 | 44% helix, 16% strand | Q0WKM4 |
| I | Serine acetyltransferase (EC 2.3.1.30) | protein | 272 | 43% helix, 15% strand | Q0WKM4 |
| K | Serine acetyltransferase (EC 2.3.1.30) | protein | 260 | 44% helix, 17% strand | Q0WKM4 |
Ligands and binding sites
- CYS · Cysteine · ligand · 12 copies · chains A, C, B, D, F, E, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- GOL · Glycerol · additive · 5 copies · chains B, C, E, F, D, H, I, J
- ACY · Acetic acid · additive · 4 copies · chains A, B, C, J, L, K
- PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · chains C
- PEG · Di(hydroxyethyl)ether · additive · chains J, 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 | 846 | 0.87 | 0.89 | 104 | SO4 |
| 2 | 451 | 0.82 | 0.89 | 60 | empty |
| 3 | 388 | 0.81 | 0.89 | 47 | empty |
| 4 | 230 | 0.80 | 0.93 | 57 | GOL, CYS |
| 5 | 345 | 0.80 | 0.90 | 49 | empty |
Interfaces
34 interfaces between chains.
- E–F · 1436 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1422 Ų buried · 11 hydrogen bonds · protein-protein
- J–L · 1419 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 1398 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1392 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3GVD · Crystal Structure of Serine Acetyltransferase CysE from Yersinia pestis · the same entry in another collection · chain B against B, 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 Q0WKM4
- Elsewhere: RCSB PDB 3GVD · PDBe 3GVD · UniProt Q0WKM4
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