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Crystal structure of xometc, a cystathionine C-lyase-like protein from xanthomonas oryzae PV.ORYZAE
Analyse Crystal structure of xometc, a cystathionine C-lyase-like protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E6G
- Type
- protein
- Length
- 1,407 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine gamma-lyase-like protein
- UniProt
- Q5H4T8
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cystathionine gamma-lyase-like protein | protein | 368 | 37% helix, 17% strand | Q5H4T8 |
| B | Cystathionine gamma-lyase-like protein | protein | 336 | 40% helix, 18% strand | Q5H4T8 |
| D | Cystathionine gamma-lyase-like protein | protein | 335 | 41% helix, 17% strand | Q5H4T8 |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.80 | 0.83 | 109 | empty |
| 2 | 446 | 0.72 | 0.82 | 68 | empty |
| 3 | 576 | 0.70 | 0.79 | 56 | empty |
| 4 | 300 | 0.54 | 0.75 | 37 | empty |
| 5 | 216 | 0.51 | 0.76 | 38 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1802 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1779 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1374 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1354 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 791 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3E6G · Crystal structure of XometC, a cystathionine c-lyase-like protein from Xanthomonas oryzae… · 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 Q5H4T8
- Elsewhere: RCSB PDB 3E6G · PDBe 3E6G · UniProt Q5H4T8
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