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Crystal structure of cystathionine gamma synthase from xanthomonas oryzae pv. oryzae in complex with homolanthionine
Analyse Crystal structure of cystathionine gamma synthase from xanthomonas oryzae pv.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LGO
- Type
- protein
- Length
- 1,548 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine gamma-synthase
- UniProt
- Q5H1U9
- Ligands
- EBO
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cystathionine gamma-synthase | protein | 387 | 39% helix, 16% strand | Q5H1U9 |
Ligands and binding sites
- EBO · (2~{S})-2-azanyl-4-[(3~{S})-3-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonomethyl)pyridin-4-yl]methylideneamino]-4-oxidanyl-4-oxidanylidene-butyl]sulfanyl-butanoic acid · ligand · 4 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.72 | 0.85 | 55 | EBO |
| 2 | 199 | 0.71 | 0.88 | 41 | EBO |
| 3 | 289 | 0.71 | 0.85 | 59 | EBO |
| 4 | 227 | 0.71 | 0.87 | 44 | EBO |
| 5 | 154 | 0.44 | 0.75 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2686 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2652 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1835 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1815 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 997 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6LGO · Crystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in… · 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 Q5H1U9
- Elsewhere: RCSB PDB 6LGO · PDBe 6LGO · UniProt Q5H1U9
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