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Structure of the chaperonin GP146 from the bacteriophage el (pseudomonas aeruginosa) in complex with atpgammas

Analyse Structure of the chaperonin GP146 from the bacteriophage el (pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6TMX
Type: protein
Length: 7,616 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative groel-like chaperonine protein
UniProt: Q2Z0T5
Ligands: AGS, MG, K
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 1 distinct chain · 52% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N	Putative groel-like chaperonine protein	protein	544	52% helix, 14% strand	Q2Z0T5

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
MG · Magnesium ion · metal · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
K · Potassium ion · metal · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	875	0.79	0.82	79	MG, K, AGS
2	890	0.79	0.81	83	MG, K, AGS
3	947	0.79	0.81	81	MG, K, AGS
4	658	0.79	0.84	62	MG, K, AGS
5	685	0.79	0.83	61	MG, K, AGS

Interfaces

21 interfaces between chains.

H–I · 1032 Å² buried · 5 hydrogen bonds · protein-protein
K–L · 1030 Å² buried · 5 hydrogen bonds · protein-protein
H–N · 1028 Å² buried · 5 hydrogen bonds · protein-protein
I–J · 1028 Å² buried · 5 hydrogen bonds · protein-protein
J–K · 1028 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6TMX · Structure of the chaperonin gp146 from the bacteriophage EL (Pseudomonas aeruginosa) in… · the same entry in another collection · 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 Q2Z0T5
Elsewhere: RCSB PDB 6TMX · PDBe 6TMX · UniProt Q2Z0T5

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