MolNFT v1 · #54884 · protein

Simocyclinone D8 bound form of tetr-like repressor simr

2Y30 · Putative repressor SIMREG2: “Simocyclinone D8 bound form of tetr-like repressor simr”. X-ray diffraction, 2 ligands (SM8, CL), 7 pockets (best druggability 0.83). MolNFT v1 #54884 on GenesisL1: 3D structure, binding sites and…

PDB: 2Y30
Type: protein
Length: 450 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative repressor SIMREG2
UniProt: Q9AMH9
Ligands: SM8, CL
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative repressor SIMREG2	protein	227	70% helix, 0% strand	Q9AMH9
B	Putative repressor SIMREG2	protein	223	75% helix, 0% strand	Q9AMH9

Ligands and binding sites

SM8 · Simocyclinone D8 · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · 6 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	499	0.83	0.89	59	SM8
2	478	0.82	0.89	63	SM8
3	216	0.69	0.86	24	empty
4	142	0.49	0.78	22	empty
5	67	0.33	0.76	16	CL

Interfaces

1 interface between chains.

A–B · 2966 Å² buried · 43 hydrogen bonds · protein-protein

Compared structures

2Y30 · Simocycli D8 bound form of TetR-like repressor SimR · the same entry in another collection · chain A against A, 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 Q9AMH9
Elsewhere: RCSB PDB 2Y30 · PDBe 2Y30 · UniProt Q9AMH9

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