MolNFT v1 · #182085 · protein
Structure of C9ORF72:SMCR8:WDR41 in complex with ARF1
7MGE · Wd repeat-containing protein 41: “Structure of C9ORF72:SMCR8:WDR41 in complex with ARF1”. Electron microscopy, 3 ligands (GDP, BEF, MG), 20 pockets (best druggability 0.84). MolNFT v1 #182085 on GenesisL1: 3D structure, binding…
- PDB
- 7MGE
- Type
- protein
- Length
- 1,322 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 41; Guanine nucleotide exchange protein SMCR8; Guanine…
- UniProt
- Q9HAD4, Q8TEV9, Q96LT7, P84077
- Ligands
- GDP, BEF, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 41 | protein | 349 | 4% helix, 38% strand | Q9HAD4 |
| B | Guanine nucleotide exchange protein SMCR8 | protein | 442 | 50% helix, 8% strand | Q8TEV9 |
| C | Guanine nucleotide exchange C9ORF72 | protein | 365 | 41% helix, 12% strand | Q96LT7 |
| E | ADP-ribosylation factor 1 | protein | 166 | 33% helix, 20% strand | P84077 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains B, E
- BEF · Beryllium trifluoride ion · ligand · chains E
- MG · Magnesium ion · metal · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.84 | 0.85 | 142 | empty |
| 2 | 1127 | 0.83 | 0.84 | 125 | empty |
| 3 | 634 | 0.81 | 0.86 | 99 | empty |
| 4 | 517 | 0.76 | 0.84 | 63 | empty |
| 5 | 227 | 0.75 | 0.89 | 37 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2030 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1225 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 348 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 256 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 167 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7MGE · Structure of C9orf72:SMCR8:WDR41 in complex with ARF1 · the same entry in another collection · chain E against E, TM-score 1.00
- Q96LT7 · AlphaFold monomer V2.0 prediction for guanine nucleotide exchange C9ORF72 (Q96LT7) · a predicted model of the same protein · chain C against A, TM-score 0.96
- Q9HAD4 · AlphaFold monomer V2.0 prediction for wd repeat-containing protein 41 (Q9HAD4) · a predicted model of the same protein · chain A against A, TM-score 0.94
- P84077 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor 1 (P84077) · a predicted model of the same protein · chain E against A, TM-score 0.91
- Q8TEV9 · AlphaFold monomer V2.0 prediction for guanine nucleotide exchange protein SMCR8 (Q8TEV9) · a predicted model of the same protein · chain B against A, TM-score 0.86
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 Q9HAD4
- Every structure of UniProt Q8TEV9
- Every structure of UniProt Q96LT7
- Every structure of UniProt P84077
- Elsewhere: RCSB PDB 7MGE · PDBe 7MGE · UniProt Q9HAD4 · UniProt Q8TEV9 · UniProt Q96LT7 · UniProt P84077
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