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Cryo-EM structure of bsclpp-ADEP1 complex at pH 6.5

Analyse Cryo-EM structure of bsclpp-ADEP1 complex at pH 6.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7FEP
Type: protein
Length: 2,730 residues
Chains: 28
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent clp protease proteolytic subunit; ADEP1
EC: 3.4.21.92
UniProt: P80244
Ligands: OTT
Pockets: 20 · best druggability 0.71

Structure

electron microscopy · 2 distinct chains · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, I, J, K, L, M, N, H	ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92)	protein	189	42% helix, 22% strand	P80244
O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b	ADEP1	protein	6	0% helix, 0% strand	—

Ligands and binding sites

OTT · (2E,4E,6E)-octa-2,4,6-trienoic acid · ligand · 14 copies · chains B, C, O, D, P, E, Q, F, R, G, S, N, H, T, I, U, J, V, K, W, L, X, M, Y, A, 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	285	0.71	0.85	39	empty
2	307	0.70	0.83	38	empty
3	383	0.67	0.80	67	empty
4	348	0.66	0.81	66	empty
5	319	0.66	0.81	52	empty

Interfaces

61 interfaces between chains.

I–J · 1290 Å² buried · 5 hydrogen bonds · protein-protein
I–H · 1272 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1265 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 1265 Å² buried · 5 hydrogen bonds · protein-protein
M–N · 1264 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 modified, 14 covalent (nonstandard, covalent ligand).

Compared structures

7FEP · Cryo-EM structure of BsClpP-ADEP1 complex at pH 6.5 · the same entry in another collection · chain L against L, 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 P80244
Elsewhere: RCSB PDB 7FEP · PDBe 7FEP · UniProt P80244

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