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CCMK2 - form 1 dodecamer

Analyse CCMK2 - form 1 dodecamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SSQ
Type: protein
Length: 602 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carbon dioxide concentrating mechanism protein
UniProt: Q8DKB2
Ligands: CL
Pockets: 1 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Carbon dioxide concentrating mechanism protein	protein	101	39% helix, 34% strand	Q8DKB2
B, C, D, F	Carbon dioxide concentrating mechanism protein	protein	100	41% helix, 31% strand	Q8DKB2

Ligands and binding sites

CL · Chloride ion · ion · 4 copies · chains A, B, D, E, F
GOL · Glycerol · additive · chains A, B, C, D, E, F

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	235	0.47	0.74	24	GOL

Interfaces

6 interfaces between chains.

A–B · 1163 Å² buried · 15 hydrogen bonds · protein-protein
D–E · 1150 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1146 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1146 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 1140 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

3SSQ · CcmK2 - form 1 dodecamer · the same entry in another collection · chain F against F, TM-score 1.00
Q8DKB2 · AlphaFold monomer V2.0 prediction for carboxysome shell protein CCMK2 (Q8DKB2) · a predicted model of the same protein · chain D 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 Q8DKB2
Elsewhere: RCSB PDB 3SSQ · PDBe 3SSQ · UniProt Q8DKB2

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