MolNFT v1 · #69541 · protein

Structure of clpp in complex with ADEP2 in triclinic crystal form

3KTK · ATP-dependent clp protease proteolytic subunit: “Structure of clpp in complex with ADEP2 in triclinic crystal form”. X-ray diffraction, 1 ligand (CXP), 20 pockets (best druggability 0.60). MolNFT v1 #69541 on GenesisL1: 3D…

PDB: 3KTK
Type: protein
Length: 2,520 residues
Chains: 28
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent clp protease proteolytic subunit; Acyldepsipeptide 2
EC: 3.4.21.92
UniProt: P80244
Ligands: CXP
Pockets: 20 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N	ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92)	protein	174	48% helix, 25% strand	P80244
O, P, Q, R, S, T, U, V, W, X, Y, Z, 0, 1	Acyldepsipeptide 2	protein	6	0% helix, 0% strand	—

Ligands and binding sites

CXP · Cyclohexane propionic acid · ligand · 14 copies · chains A, B, O, G, P, E, F, Q, C, R, D, S, T, U, H, I, V, N, W, L, M, X, J, Y, K, Z, 0, 1

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	61	0.60	0.90	18	empty
2	60	0.59	0.90	19	empty
3	52	0.58	0.91	16	empty
4	51	0.58	0.91	17	empty
5	263	0.58	0.78	47	empty

Interfaces

63 interfaces between chains.

A–B · 1067 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 1057 Å² buried · 9 hydrogen bonds · protein-protein
H–I · 1057 Å² buried · 10 hydrogen bonds · protein-protein
M–N · 1055 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 1051 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 42 modified, 14 covalent (nonstandard, covalent ligand).

Compared structures

3KTK · Structure of ClpP in complex with ADEP2 in triclinic crystal form · the same entry in another collection · chain Q against Q, 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 3KTK · PDBe 3KTK · UniProt P80244

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