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Crystal structure of YPT32 in complex with gppnhp

Analyse Crystal structure of YPT32 in complex with gppnhp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RWM
Type: protein
Length: 179 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding protein YPT32/YPT11
UniProt: P51996
Ligands: GNP, MG
Pockets: 1 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	GTP-binding protein YPT32/YPT11	protein	179	37% helix, 26% strand	P51996

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains B
MG · Magnesium ion · metal · chains B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	124	0.49	0.80	26	GNP, MG

Compared structures

3RWM · Crystal Structure of Ypt32 in Complex with GppNHp · the same entry in another collection · chain B against B, TM-score 1.00
P51996 · AlphaFold monomer V2.0 prediction for GTP-binding protein YPT32/YPT11 (P51996) · a predicted model of the same protein · chain B 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 P51996
Elsewhere: RCSB PDB 3RWM · PDBe 3RWM · UniProt P51996

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