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Structure of halothece sp. pcc 7418 CCMK4

Analyse Structure of halothece sp. pcc 7418 CCMK4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VGU
Type: protein
Length: 618 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Microcompartments protein
UniProt: K9Y6N7
Pockets: 6 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, F	Microcompartments protein	protein	104	42% helix, 34% strand	K9Y6N7
B, E	Microcompartments protein	protein	101	41% helix, 35% strand	K9Y6N7

Pockets

6 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	157	0.57	0.82	23	empty
2	59	0.50	0.86	14	empty
3	75	0.45	0.82	17	empty
4	67	0.41	0.80	14	empty
5	55	0.31	0.76	13	empty

Interfaces

9 interfaces between chains.

D–E · 1220 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 1218 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1215 Å² buried · 12 hydrogen bonds · protein-protein
D–F · 1188 Å² buried · 12 hydrogen bonds · protein-protein
C–F · 428 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5VGU · Structure of Halothece sp. PCC 7418 CcmK4 · the same entry in another collection · chain F against F, TM-score 1.00
K9Y6N7 · AlphaFold monomer V2.0 prediction for carboxysome shell protein CCMK4 (K9Y6N7) · a predicted model of the same protein · chain F 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 K9Y6N7
Elsewhere: RCSB PDB 5VGU · PDBe 5VGU · UniProt K9Y6N7

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