MolNFT v1 · #35028 · protein

Crystal structure of N-terminal GTP-binding domain of enga from thermus thermophilus HB8

2DYK · GTP-binding protein: “Crystal structure of N-terminal GTP-binding domain of enga from thermus thermophilus HB8”. X-ray diffraction, 1 ligand (GDP), 3 pockets (best druggability 0.50). MolNFT v1 #35028 on GenesisL1: 3D structure…

PDB: 2DYK
Type: protein
Length: 300 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding protein
UniProt: Q5SIH8
Ligands: GDP
Pockets: 3 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	GTP-binding protein	protein	150	39% helix, 25% strand	Q5SIH8

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	205	0.50	0.76	35	GDP
2	131	0.43	0.76	23	empty
3	77	0.31	0.74	13	empty

Interfaces

1 interface between chains.

A–B · 581 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

2DYK · Crystal structure of N-terminal GTP-binding domain of EngA from Thermus thermophilus HB8 · 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 Q5SIH8
Elsewhere: RCSB PDB 2DYK · PDBe 2DYK · UniProt Q5SIH8

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