MolNFT v1 · #72143 · protein
SEC13/SEC16 complex, S.CEREVISIAE
3MZK · Protein transport protein SEC13: “SEC13/SEC16 complex, S.CEREVISIAE”. X-ray diffraction, 19 pockets (best druggability 0.87). MolNFT v1 #72143 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3MZK
- Type
- protein
- Length
- 1,360 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC13; Protein transport protein SEC16
- UniProt
- Q04491, P48415
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Protein transport protein SEC13 | protein | 297 | 3% helix, 56% strand | Q04491 |
| B | Protein transport protein SEC16 | protein | 385 | 59% helix, 4% strand | P48415 |
| C | Protein transport protein SEC16 | protein | 381 | 59% helix, 4% strand | P48415 |
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.87 | 0.89 | 89 | empty |
| 2 | 691 | 0.87 | 0.91 | 53 | empty |
| 3 | 338 | 0.65 | 0.80 | 33 | empty |
| 4 | 128 | 0.63 | 0.87 | 19 | empty |
| 5 | 178 | 0.63 | 0.84 | 34 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3059 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2913 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2903 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 3MZK · Sec13/Sec16 complex, S.cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
- P48415 · AlphaFold monomer V2.0 prediction for copii coat assembly protein SEC16 (P48415) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q04491 · AlphaFold monomer V2.0 prediction for protein transport protein SEC13 (Q04491) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q04491
- Every structure of UniProt P48415
- Elsewhere: RCSB PDB 3MZK · PDBe 3MZK · UniProt Q04491 · UniProt P48415
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