MolNFT v1 · #64621 · protein + RNA
Crystal structure of the G33A mutant bacillus anthracis glms ribozyme bound to GLCN6P
3G8T · U1 small nuclear ribonucleoprotein a: “Crystal structure of the G33A mutant bacillus anthracis glms ribozyme bound to GLCN6P”. X-ray diffraction, 2 ligands (GLP, MG), 20 pockets (best druggability 0.78). MolNFT v1 #64621 on…
- PDB
- 3G8T
- Type
- protein + RNA
- Length
- 974 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U1 small nuclear ribonucleoprotein a; RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U…
- UniProt
- P09012
- Ligands
- GLP, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | U1 small nuclear ribonucleoprotein a | protein | 90 | 30% helix, 26% strand | P09012 |
| E, F, G, H | RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3') | rna | 13 | — | — |
| P, Q, R, S | Glms glucosamine-6-phosphate activated ribozyme | rna | 141 | — | — |
| D | U1 small nuclear ribonucleoprotein a | protein | 88 | 26% helix, 27% strand | P09012 |
Ligands and binding sites
- GLP · 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose · ligand · 4 copies · chains E, P, F, Q, G, R, H, S
- MG · Magnesium ion · metal · 10 copies · chains P, F, R, Q, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.78 | 0.81 | 66 | empty |
| 2 | 1165 | 0.75 | 0.79 | 64 | GLP |
| 3 | 623 | 0.75 | 0.82 | 45 | empty |
| 4 | 738 | 0.74 | 0.81 | 55 | GLP, MG |
| 5 | 468 | 0.73 | 0.84 | 32 | empty |
Interfaces
22 interfaces between chains.
- F–Q · 1246 Ų buried · 87 hydrogen bonds · nucleic-nucleic
- G–R · 1241 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- H–S · 1209 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- E–P · 1175 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- B–Q · 1069 Ų buried · 25 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified (nucleotide modification).
Compared structures
- 3G8T · Crystal structure of the G33A mutant Bacillus anthracis glmS ribozyme bound to GlcN6P · 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 P09012
- Elsewhere: RCSB PDB 3G8T · PDBe 3G8T · UniProt P09012
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