MolNFT v1 · #116328 · protein

Crystal structure of chaperonin groel from

5DA8 · 60 kda chaperonin: “Crystal structure of chaperonin groel from”. X-ray diffraction, 3 ligands (CA, MG, SO4), 20 pockets (best druggability 0.79). MolNFT v1 #116328 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DA8
Type: protein
Length: 13,984 residues
Chains: 28
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 60 kda chaperonin
UniProt: Q8KF02
Ligands: CA, MG, SO4
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 28 distinct chains · 51% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	60 kda chaperonin	protein	499	53% helix, 17% strand	Q8KF02
B	60 kda chaperonin	protein	519	53% helix, 18% strand	Q8KF02
C	60 kda chaperonin	protein	478	53% helix, 17% strand	Q8KF02
D	60 kda chaperonin	protein	517	52% helix, 17% strand	Q8KF02
E	60 kda chaperonin	protein	509	52% helix, 17% strand	Q8KF02
F	60 kda chaperonin	protein	497	52% helix, 18% strand	Q8KF02
G	60 kda chaperonin	protein	499	52% helix, 16% strand	Q8KF02
H	60 kda chaperonin	protein	515	53% helix, 18% strand	Q8KF02
I	60 kda chaperonin	protein	512	52% helix, 18% strand	Q8KF02
J	60 kda chaperonin	protein	507	49% helix, 18% strand	Q8KF02
K	60 kda chaperonin	protein	433	52% helix, 14% strand	Q8KF02
L	60 kda chaperonin	protein	484	52% helix, 18% strand	Q8KF02
M	60 kda chaperonin	protein	463	53% helix, 16% strand	Q8KF02
N	60 kda chaperonin	protein	511	49% helix, 17% strand	Q8KF02
O	60 kda chaperonin	protein	492	49% helix, 17% strand	Q8KF02
P	60 kda chaperonin	protein	522	52% helix, 17% strand	Q8KF02
Q	60 kda chaperonin	protein	502	51% helix, 18% strand	Q8KF02
R	60 kda chaperonin	protein	502	51% helix, 18% strand	Q8KF02
S	60 kda chaperonin	protein	512	50% helix, 18% strand	Q8KF02
T	60 kda chaperonin	protein	497	51% helix, 16% strand	Q8KF02
U	60 kda chaperonin	protein	518	53% helix, 18% strand	Q8KF02
V	60 kda chaperonin	protein	500	49% helix, 17% strand	Q8KF02
W	60 kda chaperonin	protein	517	49% helix, 18% strand	Q8KF02
X	60 kda chaperonin	protein	504	50% helix, 17% strand	Q8KF02
Y	60 kda chaperonin	protein	512	50% helix, 17% strand	Q8KF02
Z	60 kda chaperonin	protein	518	52% helix, 17% strand	Q8KF02
a	60 kda chaperonin	protein	522	52% helix, 17% strand	Q8KF02
b	60 kda chaperonin	protein	423	51% helix, 16% strand	Q8KF02

Ligands and binding sites

CA · Calcium ion · metal · 18 copies · chains A, B, F, G, I, J, K, M, N, O, P, Q, R, T, U, V, Y, Z, a
MG · Magnesium ion · metal · 7 copies · chains H, M, Q, R, S, T, V
SO4 · Sulfate ion · ion · 21 copies · chains A, B, C, D, E, F, G, J, K, L, M, N, P, R, T, U, V, Y, Z, a, b

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	1021	0.79	0.81	106	SO4
2	1093	0.78	0.80	105	empty
3	1080	0.78	0.80	104	SO4
4	1023	0.78	0.80	115	CA, SO4
5	1009	0.78	0.80	91	SO4

Interfaces

60 interfaces between chains.

H–N · 1568 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1537 Å² buried · 17 hydrogen bonds · protein-protein
Z–a · 1516 Å² buried · 21 hydrogen bonds · protein-protein
P–Q · 1491 Å² buried · 21 hydrogen bonds · protein-protein
O–P · 1464 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

5DA8 · Crystal structure of chaperonin GroEL from · 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 Q8KF02
Elsewhere: RCSB PDB 5DA8 · PDBe 5DA8 · UniProt Q8KF02

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