MolNFT v1 · #165193 · protein

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

6TMX · Putative groel-like chaperonine protein: “Structure of the chaperonin GP146 from the bacteriophage el (pseudomonas aeruginosa) in complex with atpgammas”. Electron microscopy, 3 ligands (AGS, MG, K), 20 pockets (best druggability…

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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