MolNFT v1 · #24380 · protein + RNA
The structure of the TRP RNA-binding attenuation protein (trap) bound to a 63-nucleotide RNA molecule containing gaguuu repeats
1UTD · 5'-R(*GP*UP*UP*UP*GP*AP)-3': “The structure of the TRP RNA-binding attenuation protein (trap) bound to a 63-nucleotide RNA molecule…”. X-ray diffraction, 1 ligand (TRP), 20 pockets (best druggability 0.85). MolNFT v1 #24380 on…
- PDB
- 1UTD
- Type
- protein + RNA
- Length
- 1,583 residues
- Chains
- 33
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*GP*UP*UP*UP*GP*AP)-3'; Transcription attenuation protein mtrb
- UniProt
- Q9X6J6
- Ligands
- TRP
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 0% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | 5'-R(*GP*UP*UP*UP*GP*AP)-3' | rna | 6 | — | — |
| 1 | 5'-R(*GP*UP*UP*UP*GP*AP)-3' | rna | 2 | — | — |
| 2, 3, 4, 5, 6, 7, 8, 9, Z | 5'-R(*GP*UP*UP*UP*GP*AP)-3' | rna | 3 | — | — |
| A, C, E, F, G, I, K, M, N, P, S, T, U, V | Transcription attenuation protein mtrb | protein | 70 | 0% helix, 60% strand | Q9X6J6 |
| B, D, H, J, L, O, Q, R | Transcription attenuation protein mtrb | protein | 71 | 0% helix, 59% strand | Q9X6J6 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 22 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.85 | 0.86 | 167 | TRP |
| 2 | 95 | 0.77 | 0.98 | 21 | TRP |
| 3 | 86 | 0.77 | 0.99 | 19 | TRP |
| 4 | 89 | 0.77 | 0.98 | 19 | TRP |
| 5 | 97 | 0.77 | 0.98 | 21 | TRP |
Interfaces
99 interfaces between chains.
- A–B · 1267 Ų buried · 21 hydrogen bonds · protein-protein
- H–I · 1229 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1225 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1223 Ų buried · 19 hydrogen bonds · protein-protein
- I–J · 1221 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1UTD · The structure of the trp RNA-binding attenuation protein (TRAP) bound to a 63-nucleotide… · the same entry in another collection · chain U against U, 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 Q9X6J6
- Elsewhere: RCSB PDB 1UTD · PDBe 1UTD · UniProt Q9X6J6
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