Research workbench
2.8 a crystal structure of a GET3-GET4-GET5 intermediate complex from S.CEREVISIAE
Analyse 2.8 a crystal structure of a GET3-GET4-GET5 intermediate complex from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BW8
- Type
- protein
- Length
- 971 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATPase GET3; Golgi to er traffic protein 4; Ubiquitin-like protein MDY2; Unknown protein
- EC
- 3.6.-.-
- UniProt
- B3LGZ3, Q12125, Q12285
- Ligands
- ZN
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATPase GET3 (EC 3.6.-.-) | protein | 320 | 52% helix, 13% strand | B3LGZ3 |
| B | ATPase GET3 (EC 3.6.-.-) | protein | 304 | 50% helix, 14% strand | B3LGZ3 |
| C | Golgi to er traffic protein 4 | protein | 283 | 74% helix, 5% strand | Q12125 |
| D | Ubiquitin-like protein MDY2 | protein | 51 | 39% helix, 2% strand | Q12285 |
| Z | Unknown protein | protein | 13 | 54% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.80 | 0.82 | 85 | empty |
| 2 | 93 | 0.69 | 0.93 | 23 | empty |
| 3 | 279 | 0.67 | 0.83 | 40 | empty |
| 4 | 92 | 0.66 | 0.91 | 23 | empty |
| 5 | 128 | 0.49 | 0.79 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2546 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1100 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 714 Ų buried · 8 hydrogen bonds · protein-protein
- B–Z · 284 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5BW8 · 2.8 A crystal structure of a Get3-Get4-Get5 intermediate complex from S.cerevisiae · the same entry in another collection · chain Z against Z, TM-score 1.00
- Q12125 · AlphaFold monomer V2.0 prediction for golgi to er traffic protein 4 (Q12125) · a predicted model of the same protein · chain C against A, TM-score 0.99
- B3LGZ3 · AlphaFold monomer V2.0 prediction for ATPase GET3 (B3LGZ3) · a predicted model of the same protein · chain B against A, TM-score 0.88
- Q12285 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein MDY2 (Q12285) · a predicted model of the same protein · chain D against A, TM-score 0.54
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 B3LGZ3
- Every structure of UniProt Q12125
- Every structure of UniProt Q12285
- Elsewhere: RCSB PDB 5BW8 · PDBe 5BW8 · UniProt B3LGZ3 · UniProt Q12125 · UniProt Q12285
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