MolNFT v1 · #106042 · protein

Crystal structure of an esterase RHEST1 from rhodococcus sp. ECU1013

4RNC: “Crystal structure of an esterase RHEST1 from rhodococcus sp. ECU1013”. X-ray diffraction, 1 ligand (PO4), 6 pockets (best druggability 0.76). MolNFT v1 #106042 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4RNC
Type: protein
Length: 831 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Esterase
Ligands: PO4
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Esterase	protein	281	40% helix, 19% strand	—
B, C	Esterase	protein	275	44% helix, 19% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 3 copies · chains A, B, C

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

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	838	0.76	0.80	92	PO4
2	441	0.70	0.81	53	empty
3	357	0.64	0.79	39	empty
4	204	0.62	0.82	28	empty
5	79	0.53	0.85	19	PO4

Interfaces

2 interfaces between chains.

A–B · 1462 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 504 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4RNC · Crystal structure of an esterase RhEst1 from Rhodococcus sp. ECU1013 · 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
Elsewhere: RCSB PDB 4RNC · PDBe 4RNC

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