MolNFT v1 · #47966 · protein

Crystal structure of rbcx in complex with substrate

2PEM · ORF134: “Crystal structure of rbcx in complex with substrate”. X-ray diffraction, 2 pockets (best druggability 0.51). MolNFT v1 #47966 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2PEM
Type: protein
Length: 668 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ORF134; Rbcl
UniProt: Q44177, Q44176
Pockets: 2 · best druggability 0.51

Structure

x-ray diffraction · 7 distinct chains · 86% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ORF134	protein	110	89% helix, 0% strand	Q44177
B	ORF134	protein	111	85% helix, 0% strand	Q44177
C	ORF134	protein	110	90% helix, 0% strand	Q44177
D	ORF134	protein	108	90% helix, 0% strand	Q44177
E	ORF134	protein	112	84% helix, 0% strand	Q44177
F	ORF134	protein	110	84% helix, 0% strand	Q44177
R	Rbcl	protein	7	0% helix, 0% strand	Q44176

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	156	0.51	0.79	21	empty
2	198	0.46	0.74	24	empty

Interfaces

9 interfaces between chains.

A–B · 2650 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 2496 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 2490 Å² buried · 25 hydrogen bonds · protein-protein
C–F · 440 Å² buried · 13 hydrogen bonds · protein-protein
B–R · 377 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2PEM · Crystal structure of RbcX in complex with substrate · the same entry in another collection · chain R against R, TM-score 1.00
Q44177 · AlphaFold monomer V2.0 prediction for rubisco chaperone rbcx (Q44177) · a predicted model of the same protein · chain D 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 Q44177
Every structure of UniProt Q44176
Elsewhere: RCSB PDB 2PEM · PDBe 2PEM · UniProt Q44177 · UniProt Q44176

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