Research workbench
Structure of the TRP RNA-binding attenuation protein (trap) bound to an RNA molecule containing 11 gagcc repeats
Analyse Structure of the TRP RNA-binding attenuation protein (trap) bound to an RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GTN
- Type
- protein + RNA
- Length
- 1,573 residues
- Chains
- 23
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRP RNA-binding attenuation protein; (GAGCC)11G 56-nucleotide RNA
- UniProt
- Q9X6J6
- Ligands
- TRP
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 0% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, J | TRP RNA-binding attenuation protein | protein | 68 | 0% helix, 62% strand | Q9X6J6 |
| B, C | TRP RNA-binding attenuation protein | protein | 69 | 0% helix, 61% strand | Q9X6J6 |
| D, F, H, I, K | TRP RNA-binding attenuation protein | protein | 69 | 0% helix, 61% strand | Q9X6J6 |
| G | TRP RNA-binding attenuation protein | protein | 70 | 0% helix, 60% strand | Q9X6J6 |
| L, N, P, Q, R, S, T, U, V | TRP RNA-binding attenuation protein | protein | 70 | 0% helix, 60% strand | Q9X6J6 |
| M, O | TRP RNA-binding attenuation protein | protein | 71 | 0% helix, 59% strand | Q9X6J6 |
| W | (GAGCC)11G 56-nucleotide RNA | rna | 44 | — | — |
Ligands and binding sites
- TRP · Tryptophan · ligand · 23 copies · chains A, K, B, C, D, E, F, G, H, I, J, 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 | 93 | 0.78 | 0.99 | 21 | TRP |
| 2 | 1085 | 0.78 | 0.80 | 131 | TRP |
| 3 | 640 | 0.77 | 0.83 | 86 | TRP |
| 4 | 96 | 0.77 | 0.98 | 21 | TRP |
| 5 | 95 | 0.77 | 0.98 | 20 | TRP |
Interfaces
66 interfaces between chains.
- T–U · 1217 Ų buried · 21 hydrogen bonds · protein-protein
- R–S · 1211 Ų buried · 18 hydrogen bonds · protein-protein
- N–O · 1210 Ų buried · 21 hydrogen bonds · protein-protein
- O–P · 1207 Ų buried · 20 hydrogen bonds · protein-protein
- M–N · 1207 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1GTN · Structure of the trp RNA-binding attenuation protein (TRAP) bound to an RNA molecule… · the same entry in another collection · chain K against K, 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 1GTN · PDBe 1GTN · UniProt Q9X6J6
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