Research workbench
Yeast DMC1 presynaptic complex
Analyse Yeast DMC1 presynaptic complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EJ6
- Type
- protein + DNA
- Length
- 957 residues
- Chains
- 4
- 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')
- UniProt
- A0A6L0Z498
- Ligands
- ATP, MG
- Pockets
- 10 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, A | HLJ1_G0016300.MRNA.1.CDS.1 | protein | 316 | 39% helix, 20% strand | A0A6L0Z498 |
| D | DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-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, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.83 | 0.87 | 86 | ATP, MG |
| 2 | 841 | 0.82 | 0.85 | 94 | MG, ATP |
| 3 | 637 | 0.72 | 0.80 | 60 | empty |
| 4 | 518 | 0.71 | 0.80 | 49 | empty |
| 5 | 336 | 0.68 | 0.82 | 34 | empty |
Interfaces
5 interfaces between chains.
- B–A · 1961 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1909 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 682 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 561 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 556 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 7EJ6 · Yeast Dmc1 presynaptic 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 7EJ6 · PDBe 7EJ6 · UniProt A0A6L0Z498
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