Research workbench
Crystal structure of the cytoplasmic domain of vancomycin resistance serine racemase vantg
Analyse Crystal structure of the cytoplasmic domain of vancomycin resistance serine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ECL
- Type
- protein
- Length
- 1,480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine racemase
- UniProt
- Q6WRY3
- Ligands
- CL, SO4
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine racemase | protein | 372 | 30% helix, 25% strand | Q6WRY3 |
| B | Serine racemase | protein | 369 | 31% helix, 25% strand | Q6WRY3 |
| C | Serine racemase | protein | 370 | 30% helix, 25% strand | Q6WRY3 |
| D | Serine racemase | protein | 369 | 30% helix, 26% strand | Q6WRY3 |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.84 | 0.85 | 128 | CL, SO4 |
| 2 | 502 | 0.82 | 0.89 | 50 | CL, SO4 |
| 3 | 543 | 0.81 | 0.87 | 56 | CL, SO4 |
| 4 | 544 | 0.80 | 0.86 | 57 | CL, SO4 |
| 5 | 468 | 0.74 | 0.83 | 63 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2813 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2632 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 4ECL · Crystal structure of the cytoplasmic domain of vancomycin resistance serine racemase VanTg · 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 Q6WRY3
- Elsewhere: RCSB PDB 4ECL · PDBe 4ECL · UniProt Q6WRY3
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