MolNFT v1 · #84612 · protein

Visualizing groel-es in the act of encapsulating a non-native substrate protein

3ZPZ · 60 kda chaperonin: “Visualizing groel-es in the act of encapsulating a non-native substrate protein”. Electron microscopy, 2 ligands (ADP, MG), 20 pockets (best druggability 0.82). MolNFT v1 #84612 on GenesisL1: 3D structure…

PDB: 3ZPZ
Type: protein
Length: 8,015 residues
Chains: 21
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 60 kda chaperonin; 10 kda chaperonin
UniProt: P0A6F5, P0A6F9
Ligands: ADP, MG
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 2 distinct chains · 43% helix, 20% 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	524	51% helix, 17% strand	P0A6F5
O, P, Q, R, S, T, U	10 kda chaperonin	protein	97	0% helix, 36% strand	P0A6F9

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 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	780	0.82	0.85	98	MG, ADP
2	731	0.81	0.85	90	MG, ADP
3	750	0.81	0.84	95	MG, ADP
4	736	0.81	0.84	89	MG, ADP
5	415	0.81	0.89	68	MG, ADP

Interfaces

49 interfaces between chains.

A–G · 1762 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1760 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1754 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1740 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 1728 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

3ZPZ · Visualizing GroEL-ES in the Act of Encapsulating a Non-Native Substrate Protein · the same entry in another collection · chain J against J, 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 3ZPZ · PDBe 3ZPZ · UniProt P0A6F5 · UniProt P0A6F9

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