Research workbench
2.6A resolution structure of mind complexed with mine (12-31) peptide
Analyse 2.6A resolution structure of mind complexed with mine (12-31) peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R9I
- Type
- protein
- Length
- 1,077 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Septum site-determining protein mind; Cell division topological specificity factor
- UniProt
- P0AEZ3, P0A734
- Ligands
- ADP
- Pockets
- 2 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Septum site-determining protein mind | protein | 257 | 40% helix, 18% strand | P0AEZ3 |
| B, C | Septum site-determining protein mind | protein | 254 | 41% helix, 17% strand | P0AEZ3 |
| E, F, H | Cell division topological specificity factor | protein | 14 | 86% helix, 0% strand | P0A734 |
| G | Cell division topological specificity factor | protein | 13 | 85% helix, 0% strand | P0A734 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.88 | 0.90 | 99 | ADP |
| 2 | 937 | 0.88 | 0.90 | 102 | ADP |
Interfaces
10 interfaces between chains.
- A–B · 1863 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1778 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 523 Ų buried · 6 hydrogen bonds · protein-protein
- C–H · 507 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 503 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3R9I · 2.6A resolution structure of MinD complexed with MinE (12-31) peptide · the same entry in another collection · chain H against H, TM-score 1.00
- P0AEZ3 · AlphaFold monomer V2.0 prediction for septum site-determining protein mind (P0AEZ3) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P0A734 · AlphaFold monomer V2.0 prediction for cell division topological specificity factor… · a predicted model of the same protein · chain G against A, TM-score 0.85
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 P0AEZ3
- Every structure of UniProt P0A734
- Elsewhere: RCSB PDB 3R9I · PDBe 3R9I · UniProt P0AEZ3 · UniProt P0A734
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