Research workbench
Structure of the standard kink turn hmkt-7 variant A2BM6A bound with AFL7AE protein
Analyse Structure of the standard kink turn hmkt-7 variant A2BM6A bound with AFL7AE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q8U
- Type
- protein + RNA
- Length
- 286 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*CP*GP*GP*CP*GP*AP*AP*GP*(6MZ) P*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*CP*G)-3'); 50S…
- UniProt
- O29494
- Ligands
- NA
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (5'-R(*CP*GP*GP*CP*GP*AP*AP*GP*(6MZ) P*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*CP*G)-3') | rna | 21 | — | — |
| C, D | 50S ribosomal protein L7AE | protein | 122 | 48% helix, 16% strand | O29494 |
Ligands and binding sites
- NA · Sodium ion · metal · 10 copies · chains A, D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.56 | 0.74 | 33 | NA |
| 2 | 51 | 0.28 | 0.74 | 11 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1484 Ų buried · 138 hydrogen bonds · nucleic-nucleic
- B–C · 480 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 457 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 270 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–D · 196 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6Q8U · Structure of the standard kink turn HmKt-7 variant A2bm6A bound with AfL7Ae protein · the same entry in another collection · chain A against A, TM-score 1.00
- O29494 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L7AE (O29494) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 O29494
- Elsewhere: RCSB PDB 6Q8U · PDBe 6Q8U · UniProt O29494
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