MolNFT v1 · #138164 · protein

Adc-7 in complex with boronic acid transition state inhibitor CR192

5WAF · Beta-lactamase: “Adc-7 in complex with boronic acid transition state inhibitor CR192”. X-ray diffraction, 1 ligand (A0Y), 13 pockets (best druggability 0.74). MolNFT v1 #138164 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5WAF
Type: protein
Length: 1,422 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: Q6DRA1
Ligands: A0Y
Pockets: 13 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase (EC 3.5.2.6)	protein	353	41% helix, 21% strand	Q6DRA1
B	Beta-lactamase (EC 3.5.2.6)	protein	358	42% helix, 20% strand	Q6DRA1
C	Beta-lactamase (EC 3.5.2.6)	protein	356	42% helix, 20% strand	Q6DRA1
D	Beta-lactamase (EC 3.5.2.6)	protein	355	42% helix, 20% strand	Q6DRA1

Ligands and binding sites

A0Y · phosphonooxy-[[[4-(1~{H}-1,2,3,4-tetrazol-5-yl)-2-(trifluoromethyl)phenyl]sulfonylamino]methyl]borinic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

13 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	790	0.74	0.79	69	empty
2	326	0.61	0.79	46	A0Y
3	395	0.61	0.76	51	empty
4	362	0.59	0.77	61	A0Y
5	296	0.59	0.78	45	empty

Interfaces

5 interfaces between chains.

B–C · 391 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 269 Å² buried · 1 hydrogen bond · protein-protein
A–B · 226 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 139 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 18 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

5WAF · ADC-7 in complex with boronic acid transition state inhibitor CR192 · 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 Q6DRA1
Elsewhere: RCSB PDB 5WAF · PDBe 5WAF · UniProt Q6DRA1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.