Research workbench
Human DMC1 post-synaptic complexes with mismatched dsdna
Analyse Human DMC1 post-synaptic complexes with mismatched dsdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C99
- Type
- protein + DNA
- Length
- 945 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Meiotic recombination protein DMC1/LIM15 homolog; DNA…
- UniProt
- Q14565
- Ligands
- ANP, CA
- Pockets
- 13 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 32% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Meiotic recombination protein DMC1/LIM15 homolog | protein | 309 | 32% helix, 17% strand | Q14565 |
| D | DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 9 | — | — |
| E | DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | dna | 9 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.83 | 0.91 | 59 | CA, ANP |
| 2 | 419 | 0.83 | 0.91 | 58 | CA, ANP |
| 3 | 380 | 0.73 | 0.84 | 38 | empty |
| 4 | 372 | 0.71 | 0.83 | 36 | empty |
| 5 | 474 | 0.67 | 0.79 | 57 | empty |
Interfaces
9 interfaces between chains.
- B–C · 2038 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1961 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 654 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–D · 574 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–D · 518 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 7C99 · Human DMC1 post-synaptic complexes with mismatched dsDNA · the same entry in another collection · chain E against E, TM-score 1.00
- Q14565 · AlphaFold monomer V2.0 prediction for meiotic recombination protein DMC1/LIM15 homolog… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 7C99 · PDBe 7C99 · UniProt Q14565
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