MolNFT v1 · #155617 · protein
Crystal structure of cystathionine gamma synthase from xanthomonas oryzae pv. oryzae in complex with aminoacrylate and cysteine
6LD8 · Cystathionine gamma-synthase: “Crystal structure of cystathionine gamma synthase from xanthomonas oryzae pv. oryzae in complex with…”. X-ray diffraction, 2 ligands (0JO, CYS), 14 pockets (best druggability 0.71). MolNFT v1 #155617…
- PDB
- 6LD8
- Type
- protein
- Length
- 1,549 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine gamma-synthase
- UniProt
- Q5H1U9
- Ligands
- 0JO, CYS
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine gamma-synthase | protein | 388 | 39% helix, 16% strand | Q5H1U9 |
| B, C, D | Cystathionine gamma-synthase | protein | 387 | 37% helix, 16% strand | Q5H1U9 |
Ligands and binding sites
- 0JO · 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid · ligand · 4 copies · chains A, D, B, C
- CYS · Cysteine · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.71 | 0.89 | 38 | 0JO, CYS |
| 2 | 288 | 0.69 | 0.84 | 59 | 0JO, CYS |
| 3 | 290 | 0.69 | 0.84 | 60 | 0JO, CYS |
| 4 | 202 | 0.68 | 0.86 | 43 | 0JO, CYS |
| 5 | 95 | 0.56 | 0.85 | 31 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2653 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 2637 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1838 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1836 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 976 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6LD8 · 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 6LD8 · PDBe 6LD8 · UniProt Q5H1U9
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