MolNFT v1 · #92733 · protein + RNA

Structural basis for marburg virus VP35 mediate immune evasion mechanisms

4GHL · Short palindromic RNA agacagcauaugcugucu: “Structural basis for marburg virus VP35 mediate immune evasion mechanisms”. X-ray diffraction, 2 ligands (MG, CL), 6 pockets (best druggability 0.59). MolNFT v1 #92733 on GenesisL1: 3D…

PDB: 4GHL
Type: protein + RNA
Length: 534 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Short palindromic RNA agacagcauaugcugucu; Polymerase cofactor VP35
UniProt: Q03039
Ligands: MG, CL
Pockets: 6 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, F	Short palindromic RNA agacagcauaugcugucu	rna	18	—	—
A	Polymerase cofactor VP35	protein	132	52% helix, 12% strand	Q03039
B, C, D	Polymerase cofactor VP35	protein	122	50% helix, 13% strand	Q03039

Ligands and binding sites

MG · Magnesium ion · metal · 11 copies · chains E, F, D, A, B, C
CL · Chloride ion · ion · 4 copies · chains B, C
EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	498	0.59	0.74	67	EDO
2	63	0.57	0.90	17	empty
3	109	0.45	0.79	26	empty
4	124	0.41	0.75	16	CL, EDO
5	54	0.39	0.81	22	empty

Interfaces

8 interfaces between chains.

E–F · 851 Å² buried · 81 hydrogen bonds · nucleic-nucleic
A–D · 577 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 550 Å² buried · 6 hydrogen bonds · protein-protein
E–D · 262 Å² buried · 8 hydrogen bonds · protein-nucleic
F–D · 261 Å² buried · 1 hydrogen bond · protein-nucleic

Compared structures

4GHL · Structural Basis for Marburg virus VP35 mediate immune evasion mechanisms · the same entry in another collection · chain E against E, 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 Q03039
Elsewhere: RCSB PDB 4GHL · PDBe 4GHL · UniProt Q03039

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