MolNFT v1 · #53055 · protein + RNA

Respiratory syncitial virus ribonucleoprotein

2WJ8: “Respiratory syncitial virus ribonucleoprotein”. X-ray diffraction, 1 ligand (BO4), 20 pockets (best druggability 0.82). MolNFT v1 #53055 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2WJ8
Type: protein + RNA
Length: 7,639 residues
Chains: 40
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein; RNA (5'-R(*CP*CP*CP*CP*CP*C)-3')
UniProt: P03418
Ligands: BO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 8 distinct chains · 59% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, E, I, K, M, P, Q, T	Nucleoprotein	protein	374	59% helix, 7% strand	P03418
B, H	Nucleoprotein	protein	375	58% helix, 7% strand	P03418
C, F, G, L	Nucleoprotein	protein	377	58% helix, 7% strand	P03418
J	Nucleoprotein	protein	370	59% helix, 7% strand	P03418
N, S	Nucleoprotein	protein	378	59% helix, 7% strand	P03418
O	Nucleoprotein	protein	373	59% helix, 7% strand	P03418
R	Nucleoprotein	protein	376	58% helix, 7% strand	P03418
a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t	RNA (5'-R(CPCPCPCPCPC)-3')	rna	7	—	—

Ligands and binding sites

BO4 · Borate ion · ion · 12 copies · chains A, B, C, D, H, I, K, L, M, N, O, T

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	1095	0.82	0.83	86	empty
2	1112	0.82	0.83	82	empty
3	1119	0.82	0.83	85	empty
4	1135	0.82	0.83	82	empty
5	1099	0.82	0.83	82	empty

Interfaces

100 interfaces between chains.

C–D · 2710 Å² buried · 34 hydrogen bonds · protein-protein
N–O · 2688 Å² buried · 33 hydrogen bonds · protein-protein
G–H · 2679 Å² buried · 35 hydrogen bonds · protein-protein
S–T · 2673 Å² buried · 33 hydrogen bonds · protein-protein
L–M · 2660 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

2WJ8 · Respiratory Syncitial Virus RiboNucleoProtein · the same entry in another collection · chain B against B, 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 P03418
Elsewhere: RCSB PDB 2WJ8 · PDBe 2WJ8 · UniProt P03418

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