MolNFT v1 · #58396 · protein
Crystal structure of S. cerevisiae GET3 in the open conformation in complex with GET1 cytosolic domain
3B2E · ATPase GET3: “Crystal structure of S. cerevisiae GET3 in the open conformation in complex with GET1 cytosolic domain”. X-ray diffraction, 1 ligand (ADP), 20 pockets (best druggability 0.88). MolNFT v1 #58396 on GenesisL1: 3D…
- PDB
- 3B2E
- Type
- protein
- Length
- 1,534 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATPase GET3; Golgi to er traffic protein 1
- EC
- 3.6.3.16
- UniProt
- P53192
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 8 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATPase GET3 (EC 3.6.3.16) | protein | 307 | 43% helix, 15% strand | — |
| E | Golgi to er traffic protein 1 | protein | 67 | 52% helix, 0% strand | P53192 |
| B | ATPase GET3 (EC 3.6.3.16) | protein | 325 | 38% helix, 14% strand | — |
| F | Golgi to er traffic protein 1 | protein | 62 | 61% helix, 0% strand | P53192 |
| C | ATPase GET3 (EC 3.6.3.16) | protein | 335 | 41% helix, 13% strand | — |
| G | Golgi to er traffic protein 1 | protein | 67 | 64% helix, 0% strand | P53192 |
| D | ATPase GET3 (EC 3.6.3.16) | protein | 307 | 44% helix, 15% strand | — |
| H | Golgi to er traffic protein 1 | protein | 64 | 55% helix, 0% strand | P53192 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.88 | 0.91 | 119 | ADP |
| 2 | 598 | 0.83 | 0.88 | 69 | ADP |
| 3 | 284 | 0.79 | 0.91 | 41 | empty |
| 4 | 221 | 0.79 | 0.93 | 34 | empty |
| 5 | 222 | 0.76 | 0.90 | 36 | empty |
Interfaces
11 interfaces between chains.
- C–D · 921 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 866 Ų buried · 2 hydrogen bonds · protein-protein
- D–H · 581 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 576 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 569 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3B2E · Crystal structure of S. cerevisiae Get3 in the open conformation in complex with Get1… · the same entry in another collection · chain C against C, TM-score 1.00
- P53192 · AlphaFold monomer V2.0 prediction for golgi to er traffic protein 1 (P53192) · a predicted model of the same protein · chain H against A, TM-score 0.92
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 P53192
- Elsewhere: RCSB PDB 3B2E · PDBe 3B2E · UniProt P53192
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