MolNFT v1 · #37969 · protein + RNA
Crystal structure of a vesicular stomatitis virus nucleocapsid-RNA complex
2GIC · 45-mer: “Crystal structure of a vesicular stomatitis virus nucleocapsid-RNA complex”. X-ray diffraction, 1 ligand (IUM), 20 pockets (best druggability 0.84). MolNFT v1 #37969 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2GIC
- Type
- protein + RNA
- Length
- 2,131 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 45-mer; Nucleocapsid protein
- UniProt
- P03521
- Ligands
- IUM
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | 45-mer | rna | 45 | — | — |
| A, E | Nucleocapsid protein | protein | 421 | 41% helix, 5% strand | P03521 |
| B | Nucleocapsid protein | protein | 415 | 42% helix, 5% strand | P03521 |
| C | Nucleocapsid protein | protein | 413 | 42% helix, 6% strand | P03521 |
| D | Nucleocapsid protein | protein | 416 | 41% helix, 5% strand | P03521 |
Ligands and binding sites
- IUM · Uranyl (VI) ion · metal · 15 copies · chains A, B, E, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.84 | 0.88 | 90 | empty |
| 2 | 962 | 0.83 | 0.85 | 98 | empty |
| 3 | 707 | 0.81 | 0.85 | 64 | empty |
| 4 | 490 | 0.81 | 0.88 | 54 | empty |
| 5 | 511 | 0.78 | 0.85 | 61 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2768 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 2768 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 2613 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2558 Ų buried · 22 hydrogen bonds · protein-protein
- R–D · 1124 Ų buried · 29 hydrogen bonds · protein-nucleic
Compared structures
- 2GIC · Crystal Structure of a vesicular stomatitis virus nucleocapsid-RNA complex · the same entry in another collection · chain R against R, 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 P03521
- Elsewhere: RCSB PDB 2GIC · PDBe 2GIC · UniProt P03521
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