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Crystal structure of the groel mutant A109C in complex with groes and ADP BEF2

Analyse Crystal structure of the groel mutant A109C in complex with groes and ADP BEF2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OPX
Type: protein
Length: 8,571 residues
Chains: 28
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 60 kda chaperonin; 10 kda chaperonin
UniProt: P0A6F5, P0A6F9
Ligands: ADP, BEF, MG, K
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 8 distinct chains · 25% helix, 32% 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	520	51% helix, 17% strand	P0A6F5
1, 2, S, T, X, Y, Z	10 kda chaperonin	protein	92	3% helix, 45% strand	P0A6F9
O	10 kda chaperonin	protein	93	3% helix, 44% strand	P0A6F9
P	10 kda chaperonin	protein	94	3% helix, 44% strand	P0A6F9
Q	10 kda chaperonin	protein	90	3% helix, 43% strand	P0A6F9
R	10 kda chaperonin	protein	92	3% helix, 43% strand	P0A6F9
U	10 kda chaperonin	protein	92	3% helix, 45% strand	P0A6F9
V, W	10 kda chaperonin	protein	93	3% helix, 44% strand	P0A6F9

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
BEF · Beryllium trifluoride ion · 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	340	0.82	0.92	54	ADP, MG, BEF, K
2	353	0.81	0.91	57	ADP, MG, BEF, K
3	326	0.81	0.91	53	ADP, MG, BEF, K
4	348	0.81	0.91	52	ADP, MG, BEF, K
5	367	0.81	0.90	56	ADP, MG, BEF, K

Interfaces

70 interfaces between chains.

I–J · 1945 Å² buried · 21 hydrogen bonds · protein-protein
J–K · 1907 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1889 Å² buried · 23 hydrogen bonds · protein-protein
A–G · 1864 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 1862 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

5OPX · Crystal structure of the GroEL mutant A109C in complex with GroES and ADP BeF2 · the same entry in another collection · chain K against K, 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 P0A6F5
Every structure of UniProt P0A6F9
Elsewhere: RCSB PDB 5OPX · PDBe 5OPX · UniProt P0A6F5 · UniProt P0A6F9

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