MolNFT v1 · #105977 · protein

Crystal structure of kkf mutant of bla G 2 protein

4RLD · Aspartic protease bla G 2: “Crystal structure of kkf mutant of bla G 2 protein”. X-ray diffraction, 2 ligands (NAG, ZN), 16 pockets (best druggability 0.84). MolNFT v1 #105977 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4RLD
Type: protein
Length: 1,320 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aspartic protease bla G 2
EC: 3.4.23.-
UniProt: P54958
Ligands: NAG, ZN
Pockets: 16 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 12% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Aspartic protease bla G 2 (EC 3.4.23.-)	protein	330	12% helix, 47% strand	P54958

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D

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

Pockets

16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1166	0.84	0.85	122	empty
2	505	0.72	0.81	48	empty
3	748	0.71	0.78	55	empty
4	736	0.70	0.77	56	empty
5	220	0.63	0.82	33	empty

Interfaces

4 interfaces between chains.

A–B · 1267 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1083 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 653 Å² buried · 1 hydrogen bond · protein-protein
B–C · 334 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

4RLD · Crystal structure of kkf mutant of bla G 2 protein · the same entry in another collection · chain D against D, TM-score 1.00
P54958 · AlphaFold monomer V2.0 prediction for aspartic protease bla G 2 (P54958) · 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 P54958
Elsewhere: RCSB PDB 4RLD · PDBe 4RLD · UniProt P54958

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