MolNFT v1 · #147227 · protein

Crystal structure of 4-methyl hopda bound to ligy from sphingobium sp. strain syk-6

6E6I · 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta…: “Crystal structure of 4-methyl hopda bound to ligy from sphingobium sp. strain syk-6”. X-ray diffraction, 2 ligands (HVS, ZN), 20 pockets (best druggability 0.80). MolNFT v1…

PDB: 6E6I
Type: protein
Length: 2,985 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta- cleavage compound hydrolase
UniProt: G2IN02
Ligands: HVS, ZN
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, I	2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta- cleavage compound hydrolase	protein	332	46% helix, 10% strand	G2IN02
F, G, H	2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta- cleavage compound hydrolase	protein	331	46% helix, 9% strand	G2IN02

Ligands and binding sites

HVS · (1Z,3E)-5-carboxy-3-methyl-5-oxo-1-phenylpenta-1,3-dien-1-olate · ligand · 9 copies · chains A, B, C, E, D, I, H, F, G
ZN · Zinc ion · metal · 9 copies · chains A, B, C, D, E, F, G, H, I

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

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	1052	0.80	0.81	84	ZN, HVS
2	543	0.76	0.83	43	HVS
3	504	0.74	0.82	44	HVS
4	576	0.74	0.81	44	HVS
5	541	0.73	0.81	45	HVS

Interfaces

17 interfaces between chains.

D–I · 2359 Å² buried · 36 hydrogen bonds · protein-protein
E–H · 2334 Å² buried · 37 hydrogen bonds · protein-protein
B–C · 2288 Å² buried · 37 hydrogen bonds · protein-protein
B–E · 936 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 935 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6E6I · Crystal structure of 4-methyl HOPDA bound to LigY from Sphingobium sp. strain SYK-6 · 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 G2IN02
Elsewhere: RCSB PDB 6E6I · PDBe 6E6I · UniProt G2IN02

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