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Crystal structure of the G33A mutant bacillus anthracis glms ribozyme bound to GLCN6P
Analyse Crystal structure of the G33A mutant bacillus anthracis glms ribozyme bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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