MolNFT v1 · #135717 · protein

Crystal structure of a complex formed between merb and dimethyltin

5U7A · Alkylmercury lyase: “Crystal structure of a complex formed between merb and dimethyltin”. X-ray diffraction, 3 ligands (ZN5, BR, PO4), 5 pockets (best druggability 0.83). MolNFT v1 #135717 on GenesisL1: 3D structure, binding sites…

PDB: 5U7A
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: ZN5, BR, PO4
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alkylmercury lyase (EC 4.99.1.2)	protein	208	41% helix, 22% strand	P77072

Ligands and binding sites

ZN5 · Dimethyltin dibromide · metal · 2 copies · chains A, B
BR · Bromide ion · ion · chains A
PO4 · Phosphate ion · ion · chains A, B

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

Pockets

5 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	847	0.83	0.86	75	PO4
2	185	0.82	0.96	24	ZN5
3	313	0.79	0.89	38	ZN5
4	121	0.41	0.75	18	empty
5	95	0.37	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 1166 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

5U7A · Crystal structure of a complex formed between MerB and Dimethyltin · the same entry in another collection · chain A against A, TM-score 1.00
P77072 · AlphaFold monomer V2.0 prediction for alkylmercury lyase (P77072) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 5U7A · PDBe 5U7A · UniProt P77072

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