MolNFT v1 · #82455 · protein
Crystal structure of hypothetical protein (GK2848) from geobacillus kaustophilus
3VNP · Hypothetical conserved protein: “Crystal structure of hypothetical protein (GK2848) from geobacillus kaustophilus”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.71). MolNFT v1 #82455 on GenesisL1: 3D structure…
- PDB
- 3VNP
- Type
- protein
- Length
- 513 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical conserved protein
- UniProt
- Q5KW03
- Ligands
- MG
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hypothetical conserved protein | protein | 171 | 15% helix, 40% strand | Q5KW03 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, C, B
- ACY · Acetic acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.71 | 0.99 | 18 | empty |
| 2 | 365 | 0.64 | 0.78 | 41 | ACY, MG |
| 3 | 349 | 0.64 | 0.79 | 42 | ACY, MG |
| 4 | 308 | 0.61 | 0.78 | 36 | MG, ACY |
Interfaces
3 interfaces between chains.
- B–C · 1103 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1092 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1077 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3VNP · Crystal structure of hypothetical protein (GK2848) from Geobacillus Kaustophilus · the same entry in another collection · chain A against A, 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 Q5KW03
- Elsewhere: RCSB PDB 3VNP · PDBe 3VNP · UniProt Q5KW03
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