Research workbench
SMG8-SMG9 complex GDP bound
Analyse SMG8-SMG9 complex GDP bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NKK
- Type
- protein
- Length
- 1,784 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein smg-8; Protein smg-9
- UniProt
- O62301, Q9XWJ1
- Ligands
- POP, GDP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein smg-8 | protein | 340 | 51% helix, 13% strand | O62301 |
| B | Protein smg-9 | protein | 256 | 38% helix, 17% strand | Q9XWJ1 |
| C | Protein smg-8 | protein | 330 | 48% helix, 13% strand | O62301 |
| D | Protein smg-9 | protein | 258 | 38% helix, 16% strand | Q9XWJ1 |
| E | Protein smg-8 | protein | 347 | 52% helix, 12% strand | O62301 |
| F | Protein smg-9 | protein | 253 | 37% helix, 18% strand | Q9XWJ1 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains D
- GDP · Guanosine-5'-diphosphate · ligand · chains F
- MG · Magnesium ion · metal · chains F
- EDO · 1,2-ethanediol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.81 | 0.82 | 103 | empty |
| 2 | 1056 | 0.80 | 0.81 | 101 | empty |
| 3 | 1148 | 0.79 | 0.80 | 111 | empty |
| 4 | 74 | 0.72 | 0.96 | 26 | empty |
| 5 | 431 | 0.66 | 0.79 | 42 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1807 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1691 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1678 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 890 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 757 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5NKK · SMG8-SMG9 complex GDP bound · the same entry in another collection · chain F against F, TM-score 1.00
- O62301 · AlphaFold monomer V2.0 prediction for protein smg-8 (O62301) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9XWJ1 · AlphaFold monomer V2.0 prediction for protein smg-9 (Q9XWJ1) · a predicted model of the same protein · chain F against A, TM-score 0.98
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 O62301
- Every structure of UniProt Q9XWJ1
- Elsewhere: RCSB PDB 5NKK · PDBe 5NKK · UniProt O62301 · UniProt Q9XWJ1
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