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Revised atomic structure fitting into a GROEL(D398A)-ATP7 cryo-EM MAP (emd 1047)

Analyse Revised atomic structure fitting into a GROEL(D398A)-ATP7 cryo-EM MAP (emd 1047) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2C7E
Type: protein
Length: 7,350 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 60 kda chaperonin
UniProt: P06139
Ligands: ATP, K, MG
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 1 distinct chain · 52% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N	60 kda chaperonin	protein	525	52% helix, 18% strand	P06139

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 7 copies · chains A, B, C, D, E, F, G
K · Potassium ion · metal · 7 copies · chains A, B, C, D, E, F, G
MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, F, G

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	979	0.79	0.81	96	K, MG, ATP
2	1031	0.77	0.79	92	K, MG, ATP
3	676	0.77	0.82	68	K, MG, ATP
4	975	0.77	0.79	88	K, MG, ATP
5	567	0.76	0.83	56	K, MG, ATP

Interfaces

28 interfaces between chains.

J–K · 1119 Å² buried · 7 hydrogen bonds · protein-protein
H–I · 1118 Å² buried · 7 hydrogen bonds · protein-protein
H–N · 1116 Å² buried · 7 hydrogen bonds · protein-protein
M–N · 1116 Å² buried · 7 hydrogen bonds · protein-protein
I–J · 1115 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

2C7E · Revised atomic structure fitting into a GROEL(D398A)-ATP7 cryo-EM MAP (emd 1047) · 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 P06139
Elsewhere: RCSB PDB 2C7E · PDBe 2C7E · UniProt P06139

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