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W228R-investigation of the impact from residues W228 and Y233 in the metallo-beta-lactamase gim-1

Analyse W228R-investigation of the impact from residues W228 and Y233 in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ACP
Type: protein
Length: 436 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gim-1 protein
UniProt: Q704V1
Ligands: ZN, MG
Pockets: 2 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gim-1 protein	protein	219	27% helix, 31% strand	Q704V1
B	Gim-1 protein	protein	217	27% helix, 31% strand	Q704V1

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A, B
MG · Magnesium ion · metal · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	327	0.57	0.76	39	empty
2	130	0.41	0.75	28	empty

Interfaces

1 interface between chains.

A–B · 607 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (oxidation).

Compared structures

5ACP · W228R-Investigation of the impact from residues W228 and Y233 in the… · 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 Q704V1
Elsewhere: RCSB PDB 5ACP · PDBe 5ACP · UniProt Q704V1

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