MolNFT v1 · #166815 · protein

Structure of oxa-48 bound to QPX7728 at 1.80 a

6V1O · Oxa family beta-lactamase: “Structure of oxa-48 bound to QPX7728 at 1.80 a”. X-ray diffraction, 3 ligands (RM9, MG, CL), 5 pockets (best druggability 0.82). MolNFT v1 #166815 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6V1O
Type: protein
Length: 972 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oxa family beta-lactamase
EC: 3.5.2.6
UniProt: A0A482LRD5
Ligands: RM9, MG, CL
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oxa family beta-lactamase (EC 3.5.2.6)	protein	243	41% helix, 21% strand	A0A482LRD5
B, D	Oxa family beta-lactamase (EC 3.5.2.6)	protein	242	40% helix, 21% strand	A0A482LRD5
C	Oxa family beta-lactamase (EC 3.5.2.6)	protein	245	40% helix, 20% strand	A0A482LRD5

Ligands and binding sites

RM9 · (1aR,7bS)-5-fluoro-2-hydroxy-1,1a,2,7b-tetrahydrocyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
CL · Chloride ion · ion · 2 copies · chains A, B, C, D

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	697	0.82	0.86	99	CL
2	457	0.81	0.88	74	CL, MG
3	242	0.61	0.80	41	empty
4	61	0.38	0.79	19	RM9
5	77	0.37	0.77	17	RM9

Interfaces

5 interfaces between chains.

C–D · 1035 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 998 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 228 Å² buried · 1 hydrogen bond · protein-protein
A–C · 202 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 93 Å² buried · 1 hydrogen bond · protein-protein

Modifications

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

Compared structures

6V1O · Structure of OXA-48 bound to QPX7728 at 1.80 A · 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 A0A482LRD5
Elsewhere: RCSB PDB 6V1O · PDBe 6V1O · UniProt A0A482LRD5

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