MolNFT v1 · #147736 · protein

S.AUREUS clpc resting state, asymmetric MAP

6EM9 · ATP-dependent clp protease ATP-binding subunit clpc: “S.AUREUS clpc resting state, asymmetric MAP”. Electron microscopy, 20 pockets (best druggability 0.76). MolNFT v1 #147736 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6EM9
Type: protein
Length: 6,378 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent clp protease ATP-binding subunit clpc
UniProt: Q2YSD6
Pockets: 20 · best druggability 0.76

Structure

electron microscopy · 5 distinct chains · 48% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F, G	ATP-dependent clp protease ATP-binding subunit clpc	protein	744	47% helix, 7% strand	Q2YSD6
C, H	ATP-dependent clp protease ATP-binding subunit clpc	protein	602	49% helix, 10% strand	Q2YSD6
D, I	ATP-dependent clp protease ATP-binding subunit clpc	protein	436	52% helix, 8% strand	Q2YSD6
E	ATP-dependent clp protease ATP-binding subunit clpc	protein	664	46% helix, 8% strand	Q2YSD6
L	ATP-dependent clp protease ATP-binding subunit clpc	protein	662	46% helix, 9% strand	Q2YSD6

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	873	0.76	0.80	120	empty
2	901	0.73	0.78	126	empty
3	624	0.72	0.80	105	empty
4	989	0.71	0.76	102	empty
5	769	0.70	0.78	102	empty

Interfaces

18 interfaces between chains.

E–F · 1398 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 768 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 736 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 651 Å² buried · 12 hydrogen bonds · protein-protein
A–L · 543 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6EM9 · S.aureus ClpC resting state, asymmetric map · the same entry in another collection · chain L against L, TM-score 1.00
Q2YSD6 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease ATP- binding subunit… · a predicted model of the same protein · chain H against A, TM-score 0.79

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 Q2YSD6
Elsewhere: RCSB PDB 6EM9 · PDBe 6EM9 · UniProt Q2YSD6

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