Research workbench
Crystal structure of gltph K55C-A364C mutant crosslinked with divalent mercury
Analyse Crystal structure of gltph K55C-A364C mutant crosslinked with divalent mercury in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KBC
- Type
- protein
- Length
- 1,233 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 425AA long hypothetical proton glutamate symport protein
- UniProt
- O59010
- Ligands
- ASP, NA, HG
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 425AA long hypothetical proton glutamate symport protein | protein | 411 | 70% helix, 0% strand | O59010 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 6 copies · chains A, B, C
- HG · Mercury (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.88 | 0.91 | 52 | empty |
| 2 | 527 | 0.65 | 0.76 | 68 | empty |
| 3 | 373 | 0.62 | 0.78 | 43 | empty |
| 4 | 355 | 0.62 | 0.78 | 44 | empty |
| 5 | 332 | 0.61 | 0.78 | 47 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1091 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1078 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1068 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3KBC · Crystal structure of GltPh K55C-A364C mutant crosslinked with divalent mercury · the same entry in another collection · chain B against B, TM-score 1.00
- O59010 · AlphaFold monomer V2.0 prediction for glutamate transporter homolog (O59010) · a predicted model of the same protein · chain B against A, TM-score 0.64
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 O59010
- Elsewhere: RCSB PDB 3KBC · PDBe 3KBC · UniProt O59010
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