MolNFT v1 · #69870 · protein + RNA
Crystal structure of the bacillus anthracis glms ribozyme bound to GLC6P
3L3C · U1 small nuclear ribonucleoprotein a: “Crystal structure of the bacillus anthracis glms ribozyme bound to GLC6P”. X-ray diffraction, 2 ligands (G6P, MG), 20 pockets (best druggability 0.77). MolNFT v1 #69870 on GenesisL1: 3D…
- PDB
- 3L3C
- 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)*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)…
- UniProt
- P09012
- Ligands
- G6P, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | U1 small nuclear ribonucleoprotein a | protein | 90 | 28% helix, 27% strand | P09012 |
| E, F, G, H | RNA (5'-R(*AP*(A2M)*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
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 4 copies · chains E, P, F, Q, R, G, H, S
- MG · Magnesium ion · metal · 16 copies · chains E, P, F, Q, G, R, H, S
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 | 846 | 0.77 | 0.81 | 58 | empty |
| 2 | 1125 | 0.77 | 0.80 | 70 | empty |
| 3 | 801 | 0.76 | 0.81 | 57 | empty |
| 4 | 903 | 0.75 | 0.79 | 51 | empty |
| 5 | 364 | 0.70 | 0.83 | 37 | G6P, MG |
Interfaces
23 interfaces between chains.
- G–R · 1213 Ų buried · 83 hydrogen bonds · nucleic-nucleic
- F–Q · 1204 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- H–S · 1173 Ų buried · 85 hydrogen bonds · nucleic-nucleic
- E–P · 1151 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- B–Q · 1113 Ų buried · 33 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified (nucleotide modification).
Compared structures
- 3L3C · Crystal structure of the Bacillus anthracis glmS ribozyme bound to Glc6P · 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 3L3C · PDBe 3L3C · UniProt P09012
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