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Crystal structure of human DMC1 ATPase domain
Analyse Crystal structure of human DMC1 ATPase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R3P
- Type
- protein
- Length
- 985 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Meiotic recombination protein DMC1/LIM15 homolog
- UniProt
- Q14565
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Meiotic recombination protein DMC1/LIM15 homolog | protein | 246 | 40% helix, 26% strand | Q14565 |
| B | Meiotic recombination protein DMC1/LIM15 homolog | protein | 246 | 40% helix, 25% strand | Q14565 |
| C | Meiotic recombination protein DMC1/LIM15 homolog | protein | 247 | 40% helix, 25% strand | Q14565 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C
- P6G · Hexaethylene glycol · additive · 2 copies · chains C, D
- PG4 · Tetraethylene glycol · additive · chains C
- 1PE · Pentaethylene glycol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.73 | 0.77 | 66 | empty |
| 2 | 826 | 0.73 | 0.78 | 50 | empty |
| 3 | 276 | 0.50 | 0.74 | 40 | empty |
| 4 | 97 | 0.41 | 0.77 | 23 | empty |
| 5 | 120 | 0.40 | 0.75 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1347 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1346 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 172 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 137 Ų buried · 1 hydrogen bond · 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 Q14565
- Elsewhere: RCSB PDB 6R3P · PDBe 6R3P · UniProt Q14565
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