MolNFT v1 · #48599 · protein

RBCX

2PY8 · Hypothetical protein rbcx: “RBCX”. X-ray diffraction, 1 ligand (CL), 1 pocket (best druggability 0.52). MolNFT v1 #48599 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2PY8
Type: protein
Length: 460 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein rbcx
UniProt: Q55670
Ligands: CL
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 4 distinct chains · 86% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein rbcx	protein	120	88% helix, 0% strand	Q55670
B	Hypothetical protein rbcx	protein	114	88% helix, 0% strand	Q55670
C	Hypothetical protein rbcx	protein	123	85% helix, 0% strand	Q55670
D	Hypothetical protein rbcx	protein	103	83% helix, 0% strand	Q55670

Ligands and binding sites

CL · Chloride ion · ion · chains A
PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 3 copies · chains B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	283	0.52	0.74	39	empty

Interfaces

3 interfaces between chains.

B–C · 2419 Å² buried · 26 hydrogen bonds · protein-protein
A–D · 241 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 45 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2PY8 · RbcX · the same entry in another collection · chain D against D, TM-score 1.00
Q55670 · AlphaFold monomer V2.0 prediction for rubisco chaperone rbcx (Q55670) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 Q55670
Elsewhere: RCSB PDB 2PY8 · PDBe 2PY8 · UniProt Q55670

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