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Crystal structure of NMB1681 from neisseria meningitidis MC58, a fino- like RNA chaperone

Analyse Crystal structure of NMB1681 from neisseria meningitidis MC58, a fino- like RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MW6
Type: protein
Length: 681 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein NMB1681
UniProt: Q9JY98
Pockets: 10 · best druggability 0.60

Structure

x-ray diffraction · 6 distinct chains · 63% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized protein NMB1681	protein	122	66% helix, 7% strand	Q9JY98
B	Uncharacterized protein NMB1681	protein	94	59% helix, 9% strand	Q9JY98
C	Uncharacterized protein NMB1681	protein	112	63% helix, 9% strand	Q9JY98
D	Uncharacterized protein NMB1681	protein	118	59% helix, 7% strand	Q9JY98
E	Uncharacterized protein NMB1681	protein	119	63% helix, 7% strand	Q9JY98
F	Uncharacterized protein NMB1681	protein	116	69% helix, 7% strand	Q9JY98

Ligands and binding sites

GOL · Glycerol · additive · chains C

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	268	0.60	0.79	23	empty
2	288	0.59	0.78	25	empty
3	306	0.58	0.77	50	empty
4	216	0.51	0.76	31	empty
5	148	0.48	0.77	21	empty

Interfaces

6 interfaces between chains.

D–E · 728 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 653 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 624 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 601 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 579 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 modified (engineered).

Compared structures

3MW6 · Crystal structure of NMB1681 from Neisseria meningitidis MC58, a FinO-like RNA chaperone · the same entry in another collection · chain A against A, 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 Q9JY98
Elsewhere: RCSB PDB 3MW6 · PDBe 3MW6 · UniProt Q9JY98

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