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Mgla bound to GDP

Analyse Mgla bound to GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3T1O
Type: protein
Length: 381 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gliding protein mgla
EC: 3.6.5.2
UniProt: Q5SJ82
Ligands: GDP, MG
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gliding protein mgla (EC 3.6.5.2)	protein	192	34% helix, 26% strand	Q5SJ82
B	Gliding protein mgla (EC 3.6.5.2)	protein	189	36% helix, 26% strand	Q5SJ82

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 6 copies · chains A, B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B

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

Pockets

2 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	706	0.72	0.78	61	MPD
2	397	0.69	0.81	37	empty

Interfaces

1 interface between chains.

A–B · 509 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3T1O · MglA bound to GDP · 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 Q5SJ82
Elsewhere: RCSB PDB 3T1O · PDBe 3T1O · UniProt Q5SJ82

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