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Crystal structure of PMS2 with substrate
Analyse Crystal structure of PMS2 with substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RCK
- Type
- protein
- Length
- 590 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mismatch repair endonuclease PMS2
- EC
- 3.1.-.-
- UniProt
- P54278
- Ligands
- ATP, MG
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mismatch repair endonuclease PMS2 (EC 3.1.-.-) | protein | 303 | 35% helix, 26% strand | P54278 |
| B | Mismatch repair endonuclease PMS2 (EC 3.1.-.-) | protein | 287 | 37% helix, 28% strand | P54278 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.74 | 0.98 | 22 | empty |
| 2 | 441 | 0.72 | 0.82 | 73 | empty |
| 3 | 361 | 0.62 | 0.78 | 47 | empty |
| 4 | 107 | 0.48 | 0.80 | 22 | ATP |
| 5 | 109 | 0.46 | 0.79 | 17 | ATP |
Interfaces
1 interface between chains.
- A–B · 1180 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
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 P54278
- Elsewhere: RCSB PDB 7RCK · PDBe 7RCK · UniProt P54278
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