MolNFT v1 · #140590 · protein
Cryo-EM structure of the exocyst complex
5YFP · Exocyst complex component SEC3: “Cryo-EM structure of the exocyst complex”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #140590 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YFP
- Type
- protein
- Length
- 5,982 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exocyst complex component SEC3; Exocyst complex component SEC5; Exocyst complex component…
- UniProt
- P33332, P89102, P32844, P32855, Q06245, P22224, P19658, P38261
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 8 distinct chains · 54% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exocyst complex component SEC3 | protein | 672 | 41% helix, 0% strand | P33332 |
| B | Exocyst complex component SEC5 | protein | 928 | 52% helix, 0% strand | P89102 |
| C | Exocyst complex component SEC6 | protein | 794 | 56% helix, 0% strand | P32844 |
| D | Exocyst complex component SEC8 | protein | 954 | 52% helix, 0% strand | P32855 |
| E | Exocyst complex component SEC10 | protein | 776 | 54% helix, 0% strand | Q06245 |
| F | Exocyst complex component SEC15 | protein | 725 | 57% helix, 0% strand | P22224 |
| G | Exocyst complex component EXO70 | protein | 615 | 70% helix, 0% strand | P19658 |
| H | Exocyst complex component EXO84 | protein | 518 | 53% helix, 7% strand | P38261 |
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 | 819 | 0.85 | 0.88 | 134 | empty |
| 2 | 850 | 0.82 | 0.84 | 105 | empty |
| 3 | 969 | 0.79 | 0.81 | 112 | empty |
| 4 | 518 | 0.79 | 0.86 | 93 | empty |
| 5 | 503 | 0.78 | 0.86 | 95 | empty |
Interfaces
18 interfaces between chains.
- A–B · 2040 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1558 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 1546 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 1398 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1004 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5YFP · Cryo-EM Structure of the Exocyst Complex · the same entry in another collection · chain H against H, TM-score 1.00
- P32844 · AlphaFold monomer V2.0 prediction for exocyst complex component SEC6 (P32844) · a predicted model of the same protein · chain C against A, TM-score 0.78
- P32855 · AlphaFold monomer V2.0 prediction for exocyst complex component SEC8 (P32855) · a predicted model of the same protein · chain D against A, TM-score 0.72
- P89102 · AlphaFold monomer V2.0 prediction for exocyst complex component SEC5 (P89102) · a predicted model of the same protein · chain B against A, TM-score 0.69
- P22224 · AlphaFold monomer V2.0 prediction for exocyst complex component SEC15 (P22224) · a predicted model of the same protein · chain F against A, TM-score 0.69
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 P33332
- Every structure of UniProt P89102
- Every structure of UniProt P32844
- Every structure of UniProt P32855
- Every structure of UniProt Q06245
- Every structure of UniProt P22224
- Every structure of UniProt P19658
- Every structure of UniProt P38261
- Elsewhere: RCSB PDB 5YFP · PDBe 5YFP · UniProt P33332 · UniProt P89102 · UniProt P32844 · UniProt P32855 · UniProt Q06245 · UniProt P22224 · UniProt P19658 · UniProt P38261
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