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Crystal structure of putative cystathionine gamma-synthase from burkholderia pseudomallei in complex with plp
Analyse Crystal structure of putative cystathionine gamma-synthase from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SWH
- Type
- protein
- Length
- 1,653 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cystathionine gamma-synthase
- UniProt
- Q63LU9
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative cystathionine gamma-synthase | protein | 414 | 43% helix, 15% strand | Q63LU9 |
| B | Putative cystathionine gamma-synthase | protein | 412 | 44% helix, 15% strand | Q63LU9 |
| C | Putative cystathionine gamma-synthase | protein | 414 | 44% helix, 15% strand | Q63LU9 |
| D | Putative cystathionine gamma-synthase | protein | 413 | 44% helix, 15% strand | Q63LU9 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.85 | 0.87 | 108 | empty |
| 2 | 1180 | 0.84 | 0.85 | 110 | empty |
| 3 | 251 | 0.60 | 0.80 | 38 | EDO |
| 4 | 233 | 0.59 | 0.80 | 34 | empty |
| 5 | 254 | 0.59 | 0.79 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2285 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2283 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1780 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1733 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 892 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 7SWH · Crystal Structure of Putative cystathionine gamma-synthase from Burkholderia pseudomallei… · 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 Q63LU9
- Elsewhere: RCSB PDB 7SWH · PDBe 7SWH · UniProt Q63LU9
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