MolNFT v1 · #119729 · protein

Vibrio cholerae scaffolding protein rbma in complex with magnesium.

5G50: “Vibrio cholerae scaffolding protein rbma in complex with magnesium.”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.78). MolNFT v1 #119729 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5G50
Type: protein
Length: 462 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rbma
UniProt: C3LTH7
Ligands: MG
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 1% helix, 61% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rbma	protein	234	1% helix, 62% strand	C3LTH7
B	Rbma	protein	228	1% helix, 60% strand	C3LTH7

Ligands and binding sites

MG · Magnesium ion · metal · chains A

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

Pockets

3 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	1181	0.78	0.80	108	empty
2	156	0.50	0.78	23	empty
3	97	0.48	0.81	18	empty

Interfaces

1 interface between chains.

A–B · 2861 Å² buried · 43 hydrogen bonds · protein-protein

Compared structures

5G50 · Vibrio cholerae scaffolding protein RbmA in complex with magnesium. · 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 C3LTH7
Elsewhere: RCSB PDB 5G50 · PDBe 5G50 · UniProt C3LTH7

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