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Crystal structure of a novel rubisco-like protein from the green sulfur bacterium chlorobium tepidum

Analyse Crystal structure of a novel rubisco-like protein from the green sulfur… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YKW
Type: protein
Length: 826 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rubisco-like protein
UniProt: Q8KBL4
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rubisco-like protein	protein	414	42% helix, 20% strand	Q8KBL4
B	Rubisco-like protein	protein	412	42% helix, 19% strand	Q8KBL4

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	541	0.76	0.83	58	empty
2	419	0.72	0.82	38	empty
3	91	0.68	0.92	27	empty
4	84	0.68	0.93	25	empty

Interfaces

1 interface between chains.

A–B · 3267 Å² buried · 37 hydrogen bonds · protein-protein

Compared structures

1YKW · Crystal Structure of a Novel RuBisCO-Like Protein from the Green Sulfur Bacterium… · the same entry in another collection · chain A against A, TM-score 1.00
Q8KBL4 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase-like protein… · a predicted model of the same protein · 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 Q8KBL4
Elsewhere: RCSB PDB 1YKW · PDBe 1YKW · UniProt Q8KBL4

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