Research workbench
Porphyromonas gingivalis gingipain K (kgp) catalytic and immunoglobulin superfamily-like domains
Analyse Porphyromonas gingivalis gingipain K (kgp) catalytic and immunoglobulin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RBM
- Type
- protein
- Length
- 452 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lys-gingipain W83
- EC
- 3.4.22.47
- UniProt
- Q51817
- Ligands
- HIS, CKC, NA, CA, NI, AZI
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lys-gingipain W83 (EC 3.4.22.47) | protein | 452 | 30% helix, 25% strand | Q51817 |
Ligands and binding sites
- HIS · Histidine · ligand · chains A
- CKC · (3S)-3,7-diaminoheptan-2-one · ligand · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- NI · Nickel (II) ion · metal · chains A
- AZI · Azide ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.72 | 0.99 | 18 | empty |
| 2 | 195 | 0.63 | 0.83 | 36 | empty |
| 3 | 56 | 0.28 | 0.74 | 20 | AZI |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4RBM · Porphyromonas gingivalis gingipain K (Kgp) catalytic and immunoglobulin superfamily-like… · the same entry in another collection · chain A against A, TM-score 1.00
- Q51817 · AlphaFold monomer V2.0 prediction for lys-gingipain W83 (Q51817) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q51817
- Elsewhere: RCSB PDB 4RBM · PDBe 4RBM · UniProt Q51817
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