MolNFT v1 · #34814 · protein

Structure of PH1069 protein from pyrococcus horikoshii OT3

2DRV · UPF0130 protein PH1069: “Structure of PH1069 protein from pyrococcus horikoshii OT3”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.55). MolNFT v1 #34814 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2DRV
Type: protein
Length: 389 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: UPF0130 protein PH1069
UniProt: O58796
Ligands: SO4
Pockets: 4 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	UPF0130 protein PH1069	protein	191	43% helix, 26% strand	O58796
B	UPF0130 protein PH1069	protein	198	44% helix, 27% strand	O58796

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A

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

Pockets

4 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	177	0.55	0.80	28	empty
2	232	0.54	0.77	30	empty
3	58	0.33	0.77	13	empty
4	58	0.33	0.77	13	empty

Interfaces

1 interface between chains.

A–B · 1705 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 modified (engineered).

Compared structures

2DRV · Structure of PH1069 protein from Pyrococcus horikoshii OT3 · the same entry in another collection · chain A against A, TM-score 1.00
O58796 · AlphaFold monomer V2.0 prediction for TRNA(PHE) 7-((3-amino-3-carboxy… · a predicted model of the same protein · chain B against A, TM-score 0.97

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 O58796
Elsewhere: RCSB PDB 2DRV · PDBe 2DRV · UniProt O58796

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