Research workbench
Crystal structure of the bacillus anthracis glms ribozyme bound to MAN6P
Analyse Crystal structure of the bacillus anthracis glms ribozyme bound to MAN6P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G96
- Type
- protein + RNA
- Length
- 976 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
- 6MN, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | U1 small nuclear ribonucleoprotein a | protein | 90 | 22% helix, 27% 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 ribozyme | rna | 141 | — | — |
Ligands and binding sites
- 6MN · 2-amino-2-deoxy-6-O-phosphono-alpha-D-mannopyranose · ligand · chains F, Q
- MG · Magnesium ion · metal · 9 copies · chains Q, G, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.78 | 0.82 | 62 | MG |
| 2 | 1095 | 0.78 | 0.81 | 79 | 6MN, MG |
| 3 | 813 | 0.76 | 0.81 | 63 | empty |
| 4 | 952 | 0.72 | 0.77 | 59 | empty |
| 5 | 388 | 0.72 | 0.84 | 24 | MG |
Interfaces
23 interfaces between chains.
- G–R · 1219 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- F–Q · 1178 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- H–S · 1174 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- E–P · 1167 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- C–R · 1071 Ų buried · 35 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified (nucleotide modification).
Compared structures
- 3G96 · Crystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P · 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 3G96 · PDBe 3G96 · UniProt P09012
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