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Crystal structure of ysxc complexed with gmppnp

Analyse Crystal structure of ysxc complexed with gmppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SVW
Type: protein
Length: 379 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding protein ysxc
UniProt: P38424
Ligands: GTP, MG
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP-binding protein ysxc	protein	190	35% helix, 19% strand	P38424
B	GTP-binding protein ysxc	protein	189	33% helix, 20% strand	P38424

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

5 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	681	0.73	0.79	63	MG, GTP
2	176	0.55	0.80	34	GTP
3	111	0.46	0.79	14	empty
4	85	0.43	0.79	12	empty
5	55	0.32	0.77	14	empty

Interfaces

1 interface between chains.

A–B · 284 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1SVW · Crystal Structure of YsxC complexed with GMPPNP · the same entry in another collection · chain A against A, TM-score 1.00
P38424 · AlphaFold monomer V2.0 prediction for probable GTP-binding protein engb (P38424) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P38424
Elsewhere: RCSB PDB 1SVW · PDBe 1SVW · UniProt P38424

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