MolNFT v1 · #122729 · protein

Structure of apo oxa-143 carbapenemase

5IY2 · Beta-lactamase oxa-143: “Structure of apo oxa-143 carbapenemase”. X-ray diffraction, 3 pockets (best druggability 0.59). MolNFT v1 #122729 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IY2
Type: protein
Length: 481 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase oxa-143
UniProt: D0UHC8
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase oxa-143	protein	241	42% helix, 22% strand	D0UHC8
B	Beta-lactamase oxa-143	protein	240	42% helix, 22% strand	D0UHC8

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

3 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	120	0.59	0.85	21	empty
2	283	0.58	0.77	38	GOL
3	177	0.46	0.75	31	empty

Interfaces

1 interface between chains.

A–B · 511 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (carboxylation).

Compared structures

5IY2 · Structure of apo OXA-143 carbapenemase · 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 D0UHC8
Elsewhere: RCSB PDB 5IY2 · PDBe 5IY2 · UniProt D0UHC8

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