Research workbench
Crystal structure of the product bacillus anthracis glms ribozyme
Analyse Crystal structure of the product bacillus anthracis glms ribozyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G9C
- Type
- protein + RNA
- Length
- 966 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U1 small nuclear ribonucleoprotein a; RNA (5'-R(*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')…
- UniProt
- P09012
- Ligands
- GLP, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | U1 small nuclear ribonucleoprotein a | protein | 90 | 29% helix, 24% strand | P09012 |
| E, F, G, H | RNA (5'-R(*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3') | rna | 11 | — | — |
| P, S | Glms ribozyme | rna | 140 | — | — |
| Q, R | Glms ribozyme | rna | 141 | — | — |
Ligands and binding sites
- GLP · 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose · ligand · chains E, P
- MG · Magnesium ion · metal · 3 copies · chains E, P, F, 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 | 1090 | 0.78 | 0.81 | 85 | empty |
| 2 | 929 | 0.72 | 0.77 | 47 | empty |
| 3 | 507 | 0.72 | 0.82 | 38 | empty |
| 4 | 448 | 0.70 | 0.82 | 24 | empty |
| 5 | 635 | 0.70 | 0.79 | 45 | empty |
Interfaces
18 interfaces between chains.
- B–Q · 1134 Ų buried · 31 hydrogen bonds · protein-nucleic
- F–Q · 1054 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- G–R · 1052 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- H–S · 1032 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- D–S · 1028 Ų buried · 25 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3G9C · Crystal structure of the product Bacillus anthracis glmS ribozyme · 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 3G9C · PDBe 3G9C · UniProt P09012
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