MolNFT v1 · #49703 · protein

Carboxysome subunit, ccml

2QW7 · Carbon dioxide concentrating mechanism protein ccml: “Carboxysome subunit, ccml”. X-ray diffraction, 4 pockets (best druggability 0.81). MolNFT v1 #49703 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2QW7
Type: protein
Length: 961 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carbon dioxide concentrating mechanism protein ccml
UniProt: P72759
Pockets: 4 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, F, G, I, J	Carbon dioxide concentrating mechanism protein ccml	protein	96	8% helix, 52% strand	P72759
C	Carbon dioxide concentrating mechanism protein ccml	protein	95	8% helix, 51% strand	P72759
H	Carbon dioxide concentrating mechanism protein ccml	protein	98	8% helix, 53% strand	P72759

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains A, B, C, D, E, F, G, H, I, J

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	1018	0.81	0.83	66	GOL
2	1139	0.78	0.80	74	GOL
3	61	0.33	0.77	17	empty
4	80	0.32	0.74	16	empty

Interfaces

12 interfaces between chains.

H–I · 1233 Å² buried · 26 hydrogen bonds · protein-protein
D–E · 1226 Å² buried · 30 hydrogen bonds · protein-protein
I–J · 1223 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 1217 Å² buried · 28 hydrogen bonds · protein-protein
F–J · 1217 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

2QW7 · Carboxysome Subunit, CcmL · the same entry in another collection · chain J against J, TM-score 1.00
P72759 · AlphaFold monomer V2.0 prediction for carboxysome shell vertex protein ccml (P72759) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P72759
Elsewhere: RCSB PDB 2QW7 · PDBe 2QW7 · UniProt P72759

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