Research workbench
Native structure of xometc at pH 5.2
Analyse Native structure of xometc at pH 5.2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IXS
- Type
- protein
- Length
- 733 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine gamma-lyase-like protein
- EC
- 4.4.1.1
- UniProt
- Q5H4T8
- Ligands
- CO3
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine gamma-lyase-like protein (EC 4.4.1.1) | protein | 361 | 39% helix, 16% strand | Q5H4T8 |
| B | Cystathionine gamma-lyase-like protein (EC 4.4.1.1) | protein | 372 | 41% helix, 16% strand | Q5H4T8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.54 | 0.78 | 26 | empty |
| 2 | 69 | 0.47 | 0.83 | 14 | empty |
| 3 | 56 | 0.45 | 0.83 | 13 | empty |
| 4 | 118 | 0.40 | 0.75 | 23 | empty |
| 5 | 75 | 0.33 | 0.76 | 22 | CO3 |
Interfaces
1 interface between chains.
- A–B · 1500 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 4IXS · Native structure of xometc at ph 5.2 · 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 4IXS · PDBe 4IXS · UniProt Q5H4T8
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