Research workbench
Crystal structure of domain I10 from titin in space group P212121
Analyse Crystal structure of domain I10 from titin in space group P212121 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JDJ
- Type
- protein
- Length
- 1,428 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Titin
- EC
- 2.7.11.1
- UniProt
- Q8WZ42
- Ligands
- CA
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 7 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, H, I | Titin (EC 2.7.11.1) | protein | 91 | 7% helix, 53% strand | Q8WZ42 |
| D, F, G, L | Titin (EC 2.7.11.1) | protein | 90 | 3% helix, 49% strand | Q8WZ42 |
| E, K | Titin (EC 2.7.11.1) | protein | 89 | 3% helix, 49% strand | Q8WZ42 |
| J, M | Titin (EC 2.7.11.1) | protein | 88 | 3% helix, 53% strand | Q8WZ42 |
| N | Titin (EC 2.7.11.1) | protein | 86 | 3% helix, 49% strand | Q8WZ42 |
| O | Titin (EC 2.7.11.1) | protein | 86 | 3% helix, 53% strand | Q8WZ42 |
| P | Titin (EC 2.7.11.1) | protein | 87 | 3% helix, 53% strand | Q8WZ42 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, H, O, B, D, N, E, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.87 | 0.93 | 71 | empty |
| 2 | 549 | 0.87 | 0.93 | 62 | empty |
| 3 | 766 | 0.87 | 0.90 | 65 | empty |
| 4 | 487 | 0.86 | 0.92 | 53 | empty |
| 5 | 920 | 0.84 | 0.86 | 131 | empty |
Interfaces
49 interfaces between chains.
- D–H · 763 Ų buried · 17 hydrogen bonds · protein-protein
- A–K · 718 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 718 Ų buried · 15 hydrogen bonds · protein-protein
- C–M · 674 Ų buried · 13 hydrogen bonds · protein-protein
- G–J · 665 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5JDJ · Crystal structure of domain I10 from titin in space group P212121 · 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 Q8WZ42
- Elsewhere: RCSB PDB 5JDJ · PDBe 5JDJ · UniProt Q8WZ42
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