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M. jannaschii NEP1

Analyse M. jannaschii NEP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BBE
Type: protein
Length: 408 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosome biogenesis protein NEP1-like
UniProt: Q57977
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ribosome biogenesis protein NEP1-like	protein	204	36% helix, 25% strand	Q57977

Ligands and binding sites

GOL · Glycerol · additive · 8 copies · chains A, B

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

Pockets

6 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	196	0.67	0.85	27	GOL
2	188	0.66	0.85	24	GOL
3	88	0.62	0.89	17	GOL
4	246	0.53	0.76	38	empty
5	80	0.38	0.78	15	empty

Interfaces

1 interface between chains.

A–B · 1399 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3BBE · M. jannaschii Nep1 · the same entry in another collection · chain A against A, TM-score 1.00
Q57977 · AlphaFold monomer V2.0 prediction for ribosomal RNA small subunit methyltransferase NEP1… · a predicted model of the same protein · 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 Q57977
Elsewhere: RCSB PDB 3BBE · PDBe 3BBE · UniProt Q57977

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