Research workbench
Shigella ipaa-VBS3/TBS in complex with the talin VBS1 domain 488-512
Analyse Shigella ipaa-VBS3/TBS in complex with the talin VBS1 domain 488-512 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NL1
- Type
- protein
- Length
- 991 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Talin-1; Invasin ipaa
- UniProt
- P26039, P18010
- Ligands
- SO4, CL
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 7 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Talin-1 | protein | 141 | 79% helix, 0% strand | P26039 |
| B, E, F | Talin-1 | protein | 142 | 78% helix, 0% strand | P26039 |
| C | Talin-1 | protein | 140 | 81% helix, 0% strand | P26039 |
| G, L | Invasin ipaa | protein | 22 | 86% helix, 0% strand | P18010 |
| H, I | Invasin ipaa | protein | 23 | 83% helix, 0% strand | P18010 |
| J | Invasin ipaa | protein | 26 | 92% helix, 0% strand | P18010 |
| K | Invasin ipaa | protein | 27 | 93% helix, 0% strand | P18010 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains E, H, F, D, I
- CL · Chloride ion · ion · chains D
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.87 | 0.88 | 91 | empty |
| 2 | 678 | 0.84 | 0.88 | 68 | empty |
| 3 | 400 | 0.81 | 0.90 | 52 | empty |
| 4 | 397 | 0.81 | 0.90 | 50 | empty |
| 5 | 308 | 0.80 | 0.91 | 41 | empty |
Interfaces
20 interfaces between chains.
- D–K · 914 Ų buried · 3 hydrogen bonds · protein-protein
- C–J · 877 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 862 Ų buried · 9 hydrogen bonds · protein-protein
- F–G · 858 Ų buried · 3 hydrogen bonds · protein-protein
- E–L · 857 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5NL1 · Shigella IpaA-VBS3/TBS in complex with the Talin VBS1 domain 488-512 · 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 P26039
- Every structure of UniProt P18010
- Elsewhere: RCSB PDB 5NL1 · PDBe 5NL1 · UniProt P26039 · UniProt P18010
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