Research workbench
Yeast DMC1 post-synaptic complex
Analyse Yeast DMC1 post-synaptic complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EJ7
- Type
- protein + DNA
- Length
- 966 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLJ1_G0016300.MRNA.1.CDS.1; DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'); DNA…
- UniProt
- A0A6L0Z498
- Ligands
- ATP, MG
- Pockets
- 13 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | HLJ1_G0016300.MRNA.1.CDS.1 | protein | 316 | 37% helix, 20% strand | A0A6L0Z498 |
| 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
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains B, A, C
- MG · Magnesium ion · metal · 3 copies · chains B, A, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.81 | 0.89 | 72 | MG, ATP |
| 2 | 543 | 0.80 | 0.87 | 75 | ATP, MG |
| 3 | 306 | 0.69 | 0.84 | 39 | empty |
| 4 | 298 | 0.68 | 0.83 | 48 | empty |
| 5 | 312 | 0.67 | 0.82 | 36 | empty |
Interfaces
9 interfaces between chains.
- B–A · 1987 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1981 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 668 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 545 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–D · 534 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 13 covalent (covalent ligand).
Compared structures
- 7EJ7 · Yeast Dmc1 post-synaptic complex · the same entry in another collection · chain B against B, 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
- Every structure of UniProt A0A6L0Z498
- Elsewhere: RCSB PDB 7EJ7 · PDBe 7EJ7 · UniProt A0A6L0Z498
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