Research workbench

Carboxysome shell protein, orfa from H. neapolitanus

Analyse Carboxysome shell protein, orfa from H. neapolitanus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2RCF
Type: protein
Length: 404 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Unidentified carboxysome polypeptide
UniProt: O85043
Ligands: CL
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Unidentified carboxysome polypeptide	protein	82	6% helix, 40% strand	O85043
B, C	Unidentified carboxysome polypeptide	protein	81	10% helix, 40% strand	O85043
D, E	Unidentified carboxysome polypeptide	protein	80	11% helix, 39% strand	O85043

Ligands and binding sites

CL · Chloride ion · ion · chains A, B, C, D, E
GOL · Glycerol · additive · 3 copies · chains B, C, A

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

Pockets

3 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	1017	0.72	0.76	71	CL
2	91	0.35	0.74	14	GOL
3	79	0.35	0.75	15	GOL

Interfaces

5 interfaces between chains.

C–D · 976 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 948 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 942 Å² buried · 13 hydrogen bonds · protein-protein
A–E · 921 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 912 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

2RCF · Carboxysome Shell protein, OrfA from H. Neapolitanus · the same entry in another collection · chain E against E, TM-score 1.00
O85043 · AlphaFold monomer V2.0 prediction for carboxysome shell vertex protein CSOS4A (O85043) · a predicted model of the same protein · chain E 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 O85043
Elsewhere: RCSB PDB 2RCF · PDBe 2RCF · UniProt O85043

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