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Radiation damage to the trap-RNA complex: dose (dwd) 21.9 mgy

Analyse Radiation damage to the trap-RNA complex: dose (dwd) 21.9 mgy in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EF2
Type: protein + RNA
Length: 1,565 residues
Chains: 23
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription attenuation protein mtrb; (GAGUU)10GAG 53-nucleotide RNA
UniProt: Q9X6J6
Ligands: TRP
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 0% helix, 61% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Transcription attenuation protein mtrb	protein	69	0% helix, 61% strand	Q9X6J6
B, E, G, H, I, K	Transcription attenuation protein mtrb	protein	68	0% helix, 62% strand	Q9X6J6
D, F	Transcription attenuation protein mtrb	protein	69	0% helix, 61% strand	Q9X6J6
J	Transcription attenuation protein mtrb	protein	67	0% helix, 63% strand	Q9X6J6
L, M, N, O, P, Q, R, S, T, U, V	Transcription attenuation protein mtrb	protein	70	0% helix, 60% strand	Q9X6J6
W	(GAGUU)10GAG 53-nucleotide RNA	rna	44	—	—

Ligands and binding sites

TRP · Tryptophan · ligand · 22 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, V, M, N, O, P, Q, R, S, T, U

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	823	0.82	0.84	120	empty
2	94	0.78	0.99	21	TRP
3	86	0.76	0.98	20	TRP
4	86	0.76	0.98	19	TRP
5	87	0.76	0.98	21	TRP

Interfaces

66 interfaces between chains.

N–O · 1218 Å² buried · 16 hydrogen bonds · protein-protein
Q–R · 1197 Å² buried · 18 hydrogen bonds · protein-protein
P–Q · 1191 Å² buried · 18 hydrogen bonds · protein-protein
M–N · 1190 Å² buried · 18 hydrogen bonds · protein-protein
L–V · 1180 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

5EF2 · RADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 21.9 MGy · 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 5EF2 · PDBe 5EF2 · UniProt Q9X6J6

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