Research workbench
Complex of porphyromonas gingivalis rgpb pro- and mature domains
Analyse Complex of porphyromonas gingivalis rgpb pro- and mature domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IEF
- Type
- protein
- Length
- 2,466 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gingipain R2 pro-domain; Gingipain R2 mature domain
- EC
- 3.4.22.37
- UniProt
- P95493
- Ligands
- CA, BA, NA, MG, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gingipain R2 pro-domain | protein | 192 | 7% helix, 48% strand | P95493 |
| B | Gingipain R2 mature domain (EC 3.4.22.37) | protein | 423 | 31% helix, 28% strand | P95493 |
| C | Gingipain R2 pro-domain | protein | 195 | 7% helix, 46% strand | P95493 |
| D, F, H | Gingipain R2 mature domain (EC 3.4.22.37) | protein | 424 | 30% helix, 28% strand | P95493 |
| E | Gingipain R2 pro-domain | protein | 194 | 7% helix, 46% strand | P95493 |
| G | Gingipain R2 pro-domain | protein | 190 | 7% helix, 48% strand | P95493 |
Ligands and binding sites
- CA · Calcium ion · metal · 14 copies · chains A, B, D, C, E, F, H, G
- BA · Barium ion · metal · 4 copies · chains B, D, F, H
- NA · Sodium ion · metal · 3 copies · chains F, H
- MG · Magnesium ion · metal · chains F, H
- CL · Chloride ion · ion · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B, D
- GOL · Glycerol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.80 | 0.82 | 102 | CA |
| 2 | 989 | 0.80 | 0.81 | 97 | CA, TRS |
| 3 | 236 | 0.66 | 0.84 | 35 | empty |
| 4 | 316 | 0.66 | 0.81 | 42 | empty |
| 5 | 137 | 0.62 | 0.86 | 34 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1898 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 1836 Ų buried · 40 hydrogen bonds · protein-protein
- G–H · 1773 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1722 Ų buried · 42 hydrogen bonds · protein-protein
- B–D · 949 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
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 4IEF · PDBe 4IEF · UniProt P95493
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.