MolNFT v1 · #172115 · protein

Crystal structure of class D beta-lactamase oxa-48 in complex with meropenem

6ZRP: “Crystal structure of class D beta-lactamase oxa-48 in complex with meropenem”. X-ray diffraction, 2 ligands (DWZ, CL), 10 pockets (best druggability 0.75). MolNFT v1 #172115 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6ZRP
Type: protein
Length: 970 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: Q6XEC0
Ligands: DWZ, CL
Pockets: 10 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Beta-lactamase (EC 3.5.2.6)	protein	243	40% helix, 21% strand	Q6XEC0
B, C	Beta-lactamase (EC 3.5.2.6)	protein	242	40% helix, 21% strand	Q6XEC0

Ligands and binding sites

DWZ · (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · chains A
EDO · 1,2-ethanediol · additive · 19 copies · chains A, B, C, 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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	304	0.75	0.88	43	EDO
2	266	0.75	0.89	45	empty
3	184	0.68	0.87	40	EDO
4	513	0.68	0.78	47	empty
5	168	0.68	0.88	39	EDO

Interfaces

5 interfaces between chains.

B–C · 793 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 529 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 528 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 249 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 246 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent, 2 modified (covalent ligand, carboxylation).

Compared structures

6ZRP · Crystal structure of class D Beta-lactamase OXA-48 in complex with meropenem · 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 Q6XEC0
Elsewhere: RCSB PDB 6ZRP · PDBe 6ZRP · UniProt Q6XEC0

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