MolNFT v1 · #155616 · protein
Native structure of cystathionine gamma synthase (xometb) from xanthomonas oryzae pv. oryzae
6LD7 · Cystathionine gamma-synthase: “Native structure of cystathionine gamma synthase (xometb) from xanthomonas oryzae pv. oryzae”. X-ray diffraction, 16 pockets (best druggability 0.67). MolNFT v1 #155616 on GenesisL1: 3D structure…
- PDB
- 6LD7
- Type
- protein
- Length
- 1,547 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine gamma-synthase
- UniProt
- Q5H1U9
- Pockets
- 16 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine gamma-synthase | protein | 387 | 39% helix, 15% strand | Q5H1U9 |
| B, D | Cystathionine gamma-synthase | protein | 386 | 41% helix, 16% strand | Q5H1U9 |
| C | Cystathionine gamma-synthase | protein | 388 | 39% helix, 16% strand | Q5H1U9 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · 5 copies · chains B, C, A, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.67 | 0.79 | 56 | PEG |
| 2 | 141 | 0.63 | 0.86 | 39 | empty |
| 3 | 335 | 0.63 | 0.79 | 34 | PGE |
| 4 | 362 | 0.63 | 0.78 | 39 | PEG |
| 5 | 306 | 0.62 | 0.79 | 36 | PGE |
Interfaces
6 interfaces between chains.
- A–D · 2596 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 2568 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 1773 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1722 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 935 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 6LD7 · Native Structure of cystathionine gamma synthase (XometB) from Xanthomonas oryzae pv.… · 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 6LD7 · PDBe 6LD7 · UniProt Q5H1U9
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