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Crystal structure of the copper-bound form of merb mutant D99S

Analyse Crystal structure of the copper-bound form of merb mutant D99S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C0U
Type: protein
Length: 416 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alkylmercury lyase
EC: 4.99.1.2
UniProt: P77072
Ligands: CU, BR
Pockets: 4 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alkylmercury lyase (EC 4.99.1.2)	protein	208	39% helix, 22% strand	P77072

Ligands and binding sites

CU · Copper (II) ion · metal · 2 copies · chains A, B
BR · Bromide ion · ion · chains A

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

Pockets

4 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	933	0.81	0.83	86	empty
2	160	0.80	0.96	30	empty
3	112	0.80	0.97	20	CU
4	123	0.40	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 1045 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

P77072 · AlphaFold monomer V2.0 prediction for alkylmercury lyase (P77072) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P77072
Elsewhere: RCSB PDB 5C0U · PDBe 5C0U · UniProt P77072

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