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Mad structure of OXA10 class D beta-lactamase

Analyse Mad structure of OXA10 class D beta-lactamase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1E3U
Type: protein
Length: 970 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase oxa-10
EC: 3.5.2.6
UniProt: P14489
Ligands: AUC, SO4
Pockets: 10 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-lactamase oxa-10 (EC 3.5.2.6)	protein	243	39% helix, 23% strand	P14489
C	Beta-lactamase oxa-10 (EC 3.5.2.6)	protein	242	40% helix, 23% strand	P14489
D	Beta-lactamase oxa-10 (EC 3.5.2.6)	protein	242	40% helix, 23% strand	P14489

Ligands and binding sites

AUC · Gold (I) cyanide ion · ligand · 8 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 15 copies · chains A, C, B, D
EDO · 1,2-ethanediol · additive · 12 copies · chains A, C, B, D

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	900	0.75	0.78	123	AUC, SO4
2	117	0.70	0.92	30	EDO
3	105	0.70	0.92	30	EDO
4	104	0.68	0.91	30	SO4
5	123	0.67	0.89	35	SO4

Interfaces

3 interfaces between chains.

A–C · 1392 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 1371 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 606 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1E3U · MAD structure of OXA10 class D beta-lactamase · the same entry in another collection · chain D against D, TM-score 1.00
P14489 · AlphaFold monomer V2.0 prediction for beta-lactamase oxa-10 (P14489) · a predicted model of the same protein · 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 P14489
Elsewhere: RCSB PDB 1E3U · PDBe 1E3U · UniProt P14489

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