Research workbench
C1882 paar-repeat protein from escherichia COLI in complex with a vgrg-like beta-helix that is based on a fragment of T4 GP5
Analyse C1882 paar-repeat protein from escherichia COLI in complex with a vgrg-like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JIW
- Type
- protein
- Length
- 1,488 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tail-associated lysozyme; Putative uncharacterized protein
- EC
- 3.2.1.17
- UniProt
- P16009, Q8FHJ9
- Ligands
- MG, ZN, CL
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G, I, J, K, M, N, O | Tail-associated lysozyme (EC 3.2.1.17) | protein | 93 | 0% helix, 60% strand | P16009 |
| D, H, L, P | Putative uncharacterized protein | protein | 93 | 0% helix, 45% strand | Q8FHJ9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, E, F, G, I, J, K, M, N, O
- ZN · Zinc ion · metal · 4 copies · chains D, H, L, P
- CL · Chloride ion · ion · 3 copies · chains E, F, G, M, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.85 | 0.85 | 79 | empty |
| 2 | 1192 | 0.85 | 0.85 | 84 | empty |
| 3 | 1083 | 0.84 | 0.85 | 77 | empty |
| 4 | 1063 | 0.84 | 0.85 | 84 | empty |
| 5 | 54 | 0.74 | 1.00 | 21 | MG |
Interfaces
25 interfaces between chains.
- I–K · 3762 Ų buried · 103 hydrogen bonds · protein-protein
- M–N · 3749 Ų buried · 107 hydrogen bonds · protein-protein
- E–G · 3746 Ų buried · 114 hydrogen bonds · protein-protein
- F–G · 3723 Ų buried · 111 hydrogen bonds · protein-protein
- M–O · 3722 Ų buried · 101 hydrogen bonds · protein-protein
Compared structures
- 4JIW · c1882 PAAR-repeat protein from Escherichia coli in complex with a VgrG-like beta-helix… · 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 P16009
- Every structure of UniProt Q8FHJ9
- Elsewhere: RCSB PDB 4JIW · PDBe 4JIW · UniProt P16009 · UniProt Q8FHJ9
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