Research workbench
Structure of transferase mutant-C23S,C199S
Analyse Structure of transferase mutant-C23S,C199S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H63
- Type
- protein
- Length
- 1,222 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transferase
- Ligands
- UD1, MN
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transferase | protein | 309 | 41% helix, 20% strand | — |
| C, D | Transferase | protein | 302 | 40% helix, 22% strand | — |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 6 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.73 | 0.77 | 83 | MN, UD1 |
| 2 | 704 | 0.71 | 0.78 | 65 | empty |
| 3 | 452 | 0.69 | 0.81 | 43 | UD1, MN |
| 4 | 278 | 0.67 | 0.83 | 33 | UD1, MN |
| 5 | 290 | 0.66 | 0.82 | 36 | UD1, MN |
Interfaces
3 interfaces between chains.
- B–C · 620 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 610 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 508 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5H63 · Structure of Transferase mutant-C23S,C199S · 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
- Elsewhere: RCSB PDB 5H63 · PDBe 5H63
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