MolNFT v1 · #94820 · protein

Crystal structure of atpgs bound clpx hexamer

4I81 · ATP-dependent clp protease ATP-binding subunit clpx: “Crystal structure of atpgs bound clpx hexamer”. X-ray diffraction, 2 ligands (AGS, SO4), 14 pockets (best druggability 0.83). MolNFT v1 #94820 on GenesisL1: 3D structure, binding…

PDB: 4I81
Type: protein
Length: 1,738 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent clp protease ATP-binding subunit clpx
UniProt: P0A6H1
Ligands: AGS, SO4
Pockets: 14 · best druggability 0.83

Structure

x-ray diffraction · 6 distinct chains · 47% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-dependent clp protease ATP-binding subunit clpx	protein	295	48% helix, 11% strand	P0A6H1
B	ATP-dependent clp protease ATP-binding subunit clpx	protein	300	47% helix, 12% strand	P0A6H1
C	ATP-dependent clp protease ATP-binding subunit clpx	protein	281	45% helix, 11% strand	P0A6H1
D	ATP-dependent clp protease ATP-binding subunit clpx	protein	283	47% helix, 12% strand	P0A6H1
E	ATP-dependent clp protease ATP-binding subunit clpx	protein	290	49% helix, 11% strand	P0A6H1
F	ATP-dependent clp protease ATP-binding subunit clpx	protein	289	48% helix, 11% strand	P0A6H1

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B, D, E
SO4 · Sulfate ion · ion · 2 copies · chains C, F

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

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1058	0.83	0.83	80	AGS
2	1004	0.83	0.83	82	AGS
3	1149	0.81	0.82	109	AGS
4	938	0.81	0.83	97	SO4
5	1008	0.81	0.82	102	AGS

Interfaces

6 interfaces between chains.

A–B · 1263 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1055 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 1042 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 1010 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 966 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4I81 · Crystal Structure of ATPgS bound ClpX Hexamer · the same entry in another collection · chain F against F, TM-score 1.00
P0A6H1 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease ATP- binding subunit… · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P0A6H1
Elsewhere: RCSB PDB 4I81 · PDBe 4I81 · UniProt P0A6H1

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