Research workbench

MBP-L30

Analyse MBP-L30 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NMU
Type: protein
Length: 943 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Maltose-binding periplasmic protein; 60S ribosomal protein L30
UniProt: P02928, P14120
Ligands: GLC
Pockets: 11 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Maltose-binding periplasmic protein	protein	368	45% helix, 21% strand	P02928
B	60S ribosomal protein L30	protein	104	46% helix, 18% strand	P14120
D	60S ribosomal protein L30	protein	103	40% helix, 17% strand	P14120

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, C

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

Pockets

11 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	1097	0.74	0.77	87	empty
2	741	0.74	0.79	55	GLC
3	368	0.72	0.84	31	GLC
4	243	0.50	0.75	34	empty
5	119	0.46	0.79	37	empty

Interfaces

4 interfaces between chains.

B–C · 741 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 371 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 339 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 298 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1NMU · MBP-L30 · the same entry in another collection · chain A against A, TM-score 1.00
P14120 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L30 (P14120) · a predicted model of the same protein · chain D against A, TM-score 0.93

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 P02928
Every structure of UniProt P14120
Elsewhere: RCSB PDB 1NMU · PDBe 1NMU · UniProt P02928 · UniProt P14120

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