MolNFT v1 · #47855 · protein

Crystal structure of PH0725 from pyrococcus horikoshii OT3

2PB5 · Diphthine synthase: “Crystal structure of PH0725 from pyrococcus horikoshii OT3”. X-ray diffraction, 1 ligand (SAH), 7 pockets (best druggability 0.74). MolNFT v1 #47855 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2PB5
Type: protein
Length: 530 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diphthine synthase
EC: 2.1.1.98
UniProt: O58456
Ligands: SAH
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Diphthine synthase (EC 2.1.1.98)	protein	265	38% helix, 23% strand	O58456

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · chains A
FMT · Formic acid · additive · chains A
GOL · Glycerol · additive · chains B

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

Pockets

7 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	467	0.74	0.83	47	empty
2	399	0.73	0.83	56	SAH
3	139	0.43	0.75	19	empty
4	100	0.40	0.76	20	empty
5	101	0.40	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 2576 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

2PB5 · Crystal structure of PH0725 from Pyrococcus horikoshii OT3 · the same entry in another collection · chain A against A, TM-score 1.00
O58456 · AlphaFold monomer V2.0 prediction for diphthine synthase (O58456) · a predicted model of the same protein · chain B 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 O58456
Elsewhere: RCSB PDB 2PB5 · PDBe 2PB5 · UniProt O58456

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