Research workbench
Crystal structure of rpff complexed with rec domain of rpfc
Analyse Crystal structure of rpff complexed with rec domain of rpfc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M6M
- Type
- protein
- Length
- 1,132 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rpff protein; SENSORY/REGULATORY protein rpfc
- EC
- 2.7.13.3
- UniProt
- Q7CLS3, P0C0F6
- Ligands
- MG, IOD
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rpff protein | protein | 261 | 53% helix, 16% strand | Q7CLS3 |
| B | Rpff protein | protein | 263 | 53% helix, 16% strand | Q7CLS3 |
| C | Rpff protein | protein | 262 | 53% helix, 16% strand | Q7CLS3 |
| D | SENSORY/REGULATORY protein rpfc (EC 2.7.13.3) | protein | 118 | 47% helix, 20% strand | P0C0F6 |
| E | SENSORY/REGULATORY protein rpfc (EC 2.7.13.3) | protein | 113 | 44% helix, 19% strand | P0C0F6 |
| F | SENSORY/REGULATORY protein rpfc (EC 2.7.13.3) | protein | 115 | 44% helix, 19% strand | P0C0F6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains D, E, F
- IOD · Iodide ion · ion · 14 copies · chains A, D, B, E, C, F
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.79 | 0.85 | 48 | empty |
| 2 | 760 | 0.77 | 0.82 | 59 | empty |
| 3 | 378 | 0.77 | 0.87 | 35 | empty |
| 4 | 74 | 0.76 | 0.99 | 26 | EDO |
| 5 | 73 | 0.75 | 0.98 | 26 | EDO |
Interfaces
9 interfaces between chains.
- A–C · 962 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 961 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 945 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 826 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 819 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3M6M · Crystal structure of RpfF complexed with REC domain of RpfC · the same entry in another collection · chain F against F, TM-score 1.00
- P0C0F6 · AlphaFold monomer V2.0 prediction for SENSORY/REGULATORY protein rpfc (P0C0F6) · a predicted model of the same protein · chain F 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 Q7CLS3
- Every structure of UniProt P0C0F6
- Elsewhere: RCSB PDB 3M6M · PDBe 3M6M · UniProt Q7CLS3 · UniProt P0C0F6
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