MolNFT v1 · #113465 · protein

Crystal structure of a mutant (665SXA) C-terminal domain of rgpb

5AG9 · Gingipain R2: “Crystal structure of a mutant (665SXA) C-terminal domain of rgpb”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.47). MolNFT v1 #113465 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5AG9
Type: protein
Length: 298 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gingipain R2
EC: 3.4.22.37
UniProt: P95493
Ligands: SO4
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 63% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Gingipain R2 (EC 3.4.22.37)	protein	149	0% helix, 63% strand	P95493

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	179	0.47	0.76	30	empty
2	119	0.41	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 411 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5AG9 · CRYSTAL STRUCTURE OF A MUTANT (665sXa) C-TERMINAL DOMAIN OF RGPB · the same entry in another collection · chain A against A, TM-score 1.00
P95493 · AlphaFold monomer V2.0 prediction for gingipain R2 (P95493) · a predicted model of the same protein · chain B against A, TM-score 0.58

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 P95493
Elsewhere: RCSB PDB 5AG9 · PDBe 5AG9 · UniProt P95493

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