MolNFT v1 · #2870 · protein + RNA

Crystal structure of a complex of TRP RNA-binding attenuation protein with a 53-base single stranded RNA containing eleven gag triplets separated by au dinucleotides

1C9S · Single stranded RNA (55-mer): “Crystal structure of a complex of TRP RNA-binding attenuation protein with a 53-base single stranded RNA…”. X-ray diffraction, 1 ligand (TRP), 20 pockets (best druggability 0.86). MolNFT v1 #2870 on…

PDB: 1C9S
Type: protein + RNA
Length: 1,583 residues
Chains: 23
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Single stranded RNA (55-mer); TRP RNA-binding attenuation protein
UniProt: Q9X6J6
Ligands: TRP
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 8 distinct chains · 0% helix, 61% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
W	Single stranded RNA (55-mer)	rna	55	—	—
A, D, F, H, I, K	TRP RNA-binding attenuation protein	protein	69	0% helix, 61% strand	Q9X6J6
B, E	TRP RNA-binding attenuation protein	protein	68	0% helix, 62% strand	Q9X6J6
C	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
J	TRP RNA-binding attenuation protein	protein	67	0% helix, 63% 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

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	962	0.86	0.87	151	empty
2	92	0.77	0.98	19	TRP
3	90	0.77	0.98	21	TRP
4	91	0.77	0.98	21	TRP
5	96	0.77	0.98	22	TRP

Interfaces

66 interfaces between chains.

L–M · 1231 Å² buried · 19 hydrogen bonds · protein-protein
T–U · 1216 Å² buried · 17 hydrogen bonds · protein-protein
P–Q · 1207 Å² buried · 17 hydrogen bonds · protein-protein
N–O · 1203 Å² buried · 18 hydrogen bonds · protein-protein
U–V · 1200 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1C9S · Crystal structure of a complex of TRP RNA-binding attenuation protein with a 53-base… · the same entry in another collection · chain J against J, 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 1C9S · PDBe 1C9S · UniProt Q9X6J6

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