MolNFT v1 · #114035 · protein
Structure of MOEN5-SSO7D fusion protein in complex with geranyl pyrophosphate
5B03 · MOEN5,DNA-binding protein 7D: “Structure of MOEN5-SSO7D fusion protein in complex with geranyl pyrophosphate”. X-ray diffraction, 1 ligand (GPP), 9 pockets (best druggability 0.82). MolNFT v1 #114035 on GenesisL1: 3D structure…
- PDB
- 5B03
- Type
- protein
- Length
- 1,190 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MOEN5,DNA-binding protein 7D
- UniProt
- A0A010, P39476
- Ligands
- GPP
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MOEN5,DNA-binding protein 7D | protein | 264 | 77% helix, 0% strand | A0A010, P39476 |
| B | MOEN5,DNA-binding protein 7D | protein | 332 | 66% helix, 10% strand | A0A010, P39476 |
| C | MOEN5,DNA-binding protein 7D | protein | 261 | 80% helix, 0% strand | A0A010, P39476 |
| D | MOEN5,DNA-binding protein 7D | protein | 333 | 64% helix, 8% strand | A0A010, P39476 |
Ligands and binding sites
- GPP · Geranyl 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.82 | 0.84 | 73 | GPP |
| 2 | 1065 | 0.79 | 0.81 | 80 | GPP |
| 3 | 701 | 0.79 | 0.83 | 66 | GPP |
| 4 | 765 | 0.76 | 0.80 | 59 | GPP |
| 5 | 302 | 0.58 | 0.77 | 49 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1862 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1840 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 842 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 339 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5B03 · Structure of MoeN5-Sso7d fusion protein in complex with geranyl pyrophosphate · the same entry in another collection · chain D against D, TM-score 1.00
- P39476 · AlphaFold monomer V2.0 prediction for DNA-binding protein 7D (P39476) · a predicted model of the same protein · chain D against A, TM-score 0.19
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 A0A010
- Every structure of UniProt P39476
- Elsewhere: RCSB PDB 5B03 · PDBe 5B03 · UniProt A0A010 · UniProt P39476
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