MolNFT v1 · #41147 · protein
Portal protein (GP6) from bacteriophage SPP1
2JES: “Portal protein (GP6) from bacteriophage SPP1”. X-ray diffraction, 2 ligands (HG, CA), 20 pockets (best druggability 0.85). MolNFT v1 #41147 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2JES
- Type
- protein
- Length
- 5,200 residues
- Chains
- 26
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Portal protein; Unidentified fragment of portal protein
- UniProt
- P54309
- Ligands
- HG, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W, Y | Portal protein | protein | 370 | 52% helix, 14% strand | P54309 |
| B, D, F, H, J, L, N, P, R, T, V, X, Z | Unidentified fragment of portal protein | protein | 30 | 0% helix, 30% strand | — |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 13 copies · chains A, C, E, G, I, K, M, O, Q, S, U, W, Y
- CA · Calcium ion · metal · 13 copies · chains A, C, E, G, I, K, M, O, Q, S, U, W, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.85 | 0.90 | 68 | empty |
| 2 | 346 | 0.82 | 0.92 | 63 | empty |
| 3 | 1133 | 0.82 | 0.83 | 113 | empty |
| 4 | 258 | 0.80 | 0.92 | 39 | empty |
| 5 | 736 | 0.80 | 0.83 | 86 | empty |
Interfaces
52 interfaces between chains.
- K–M · 3467 Ų buried · 38 hydrogen bonds · protein-protein
- W–Y · 3462 Ų buried · 35 hydrogen bonds · protein-protein
- I–K · 3455 Ų buried · 36 hydrogen bonds · protein-protein
- Q–S · 3454 Ų buried · 35 hydrogen bonds · protein-protein
- U–W · 3443 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 2JES · Portal protein (gp6) from bacteriophage SPP1 · the same entry in another collection · chain L against L, 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 P54309
- Elsewhere: RCSB PDB 2JES · PDBe 2JES · UniProt P54309
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