MolNFT v1 · #134602 · protein
Immunoglobulin light chain variable domain al-T05
5T93 · Alt-05 immunoglobulin light chain variable domain from…: “Immunoglobulin light chain variable domain al-T05”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.77). MolNFT v1 #134602 on GenesisL1: 3D structure…
- PDB
- 5T93
- Type
- protein
- Length
- 440 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alt-05 immunoglobulin light chain variable domain from light chain amyloidosis patient
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alt-05 immunoglobulin light chain variable domain from light chain amyloidosis patient | protein | 110 | 7% helix, 50% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 10 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.77 | 0.80 | 85 | empty |
| 2 | 124 | 0.54 | 0.82 | 20 | ZN, ACT |
| 3 | 116 | 0.51 | 0.81 | 20 | ZN, ACT |
| 4 | 100 | 0.51 | 0.82 | 18 | ZN, ACT |
| 5 | 116 | 0.51 | 0.81 | 20 | ZN, ACT |
Interfaces
5 interfaces between chains.
- B–D · 602 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 597 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 261 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 248 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 42 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5T93 · Immunoglobulin light chain variable domain AL-T05 · 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
- Elsewhere: RCSB PDB 5T93 · PDBe 5T93
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