MolNFT v1 · #135716 · protein

Crystal structure of a complex formed between merb and dimethyltin

5U79 · Alkylmercury lyase: “Crystal structure of a complex formed between merb and dimethyltin”. X-ray diffraction, 2 ligands (ZN5, BR), 5 pockets (best druggability 0.83). MolNFT v1 #135716 on GenesisL1: 3D structure, binding sites and…

PDB: 5U79
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
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
ACT · Acetate ion · additive · 2 copies · 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	304	0.83	0.93	36	ZN5
2	321	0.82	0.92	34	ZN5
3	1033	0.82	0.83	87	ACT
4	109	0.40	0.76	14	empty
5	108	0.38	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 968 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5U79 · 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 0.99

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 5U79 · PDBe 5U79 · UniProt P77072

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