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Structure of recombinant cdh-H28AN484A

Analyse Structure of recombinant cdh-H28AN484A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4D5G
Type: protein
Length: 1,173 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclohexane-1,2-dione hydrolase
EC: 3.7.1.11
UniProt: P0CH62
Ligands: FAD, TPP, 1PG, MG
Pockets: 10 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclohexane-1,2-dione hydrolase (EC 3.7.1.11)	protein	586	41% helix, 16% strand	P0CH62
B	Cyclohexane-1,2-dione hydrolase (EC 3.7.1.11)	protein	587	40% helix, 16% strand	P0CH62

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · chains A
MG · Magnesium ion · metal · 3 copies · chains A, B
PG4 · Tetraethylene glycol · additive · 9 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
2PE · Nonaethylene glycol · additive · 2 copies · chains B

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

Pockets

10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	693	0.87	0.91	107	FAD, TPP
2	729	0.86	0.90	121	FAD, TPP, MG
3	81	0.49	0.83	16	empty
4	57	0.45	0.83	20	empty
5	150	0.42	0.75	26	PG4

Interfaces

1 interface between chains.

A–B · 5142 Å² buried · 50 hydrogen bonds · protein-protein

Compared structures

4D5G · Structure of recombinant CDH-H28AN484A · the same entry in another collection · chain A against A, TM-score 1.00
P0CH62 · AlphaFold monomer V2.0 prediction for cyclohexane-1,2-dione hydrolase (P0CH62) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P0CH62
Elsewhere: RCSB PDB 4D5G · PDBe 4D5G · UniProt P0CH62

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