Research workbench
The crystal structure of a binary complex of two pseudopilins: epsi and epsj from the type 2 secretion system of vibrio vulnificus
Analyse The crystal structure of a binary complex of two pseudopilins: epsi and epsj… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RET
- Type
- protein
- Length
- 954 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pseudopilin epsi; Epsj
- UniProt
- Q7MPZ1
- Ligands
- NA, CL
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 8 distinct chains · 20% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pseudopilin epsi | protein | 84 | 27% helix, 40% strand | Q7MPZ1 |
| B | Epsj | protein | 159 | 16% helix, 48% strand | — |
| C | Pseudopilin epsi | protein | 80 | 29% helix, 43% strand | Q7MPZ1 |
| D | Epsj | protein | 155 | 15% helix, 48% strand | — |
| E | Pseudopilin epsi | protein | 82 | 28% helix, 41% strand | Q7MPZ1 |
| F | Epsj | protein | 156 | 16% helix, 47% strand | — |
| G | Pseudopilin epsi | protein | 81 | 28% helix, 40% strand | Q7MPZ1 |
| H | Epsj | protein | 157 | 16% helix, 46% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains F, H
- CL · Chloride ion · ion · 2 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.75 | 0.86 | 55 | empty |
| 2 | 257 | 0.72 | 0.86 | 37 | CL |
| 3 | 291 | 0.71 | 0.85 | 35 | empty |
| 4 | 386 | 0.70 | 0.82 | 31 | empty |
| 5 | 242 | 0.69 | 0.85 | 36 | CL |
Interfaces
20 interfaces between chains.
- F–H · 1053 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 1051 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 766 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 758 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 753 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 2RET · The crystal structure of a binary complex of two pseudopilins: EpsI and EpsJ from the… · 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 Q7MPZ1
- Elsewhere: RCSB PDB 2RET · PDBe 2RET · UniProt Q7MPZ1
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