Research workbench
6.0 a crystal structure of a GET3-GET4-GET5 intermediate complex from S.CEREVISIAE
Analyse 6.0 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
- 5BWK
- Type
- protein
- Length
- 5,192 residues
- Chains
- 24
- 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
- EC
- 3.6.-.-
- UniProt
- B3LGZ3, Q12125, Q12285
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, M, N, O, P, C | ATPase GET3 (EC 3.6.-.-) | protein | 304 | 43% helix, 14% strand | B3LGZ3 |
| E, G, I, K, Q, S, U, W | Golgi to er traffic protein 4 | protein | 291 | 70% helix, 4% strand | Q12125 |
| F, H, J, L, R, T, V, X | Ubiquitin-like protein MDY2 | protein | 54 | 26% helix, 0% strand | Q12285 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, D, C, M, N, O, P
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 | 776 | 0.88 | 0.91 | 97 | empty |
| 2 | 1048 | 0.86 | 0.87 | 107 | empty |
| 3 | 1200 | 0.86 | 0.86 | 113 | empty |
| 4 | 1151 | 0.85 | 0.85 | 116 | empty |
| 5 | 1100 | 0.81 | 0.82 | 105 | empty |
Interfaces
34 interfaces between chains.
- U–V · 2609 Ų buried · 32 hydrogen bonds · protein-protein
- K–L · 2601 Ų buried · 33 hydrogen bonds · protein-protein
- S–T · 2598 Ų buried · 32 hydrogen bonds · protein-protein
- G–H · 2588 Ų buried · 30 hydrogen bonds · protein-protein
- W–X · 2584 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 5BWK · 6.0 A Crystal structure of a Get3-Get4-Get5 intermediate complex from S.cerevisiae · the same entry in another collection · chain K against K, TM-score 1.00
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 5BWK · PDBe 5BWK · UniProt B3LGZ3 · UniProt Q12125 · UniProt Q12285
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