MolNFT v1 · #54495 · protein
Human dynein light chain (DYNLL2) in complex with an in vitro evolved peptide (ac-srgtqte).
2XQQ · Dynein light chain 2, cytoplasmic: “Human dynein light chain (DYNLL2) in complex with an in vitro evolved peptide (ac-srgtqte).”. X-ray diffraction, 1 pocket (best druggability 0.75). MolNFT v1 #54495 on GenesisL1: 3D structure…
- PDB
- 2XQQ
- Type
- protein
- Length
- 375 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynein light chain 2, cytoplasmic; Sac-arg-gly-thr-gln-thr-glu
- UniProt
- Q96FJ2
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynein light chain 2, cytoplasmic | protein | 87 | 38% helix, 40% strand | Q96FJ2 |
| B | Dynein light chain 2, cytoplasmic | protein | 89 | 40% helix, 36% strand | Q96FJ2 |
| C | Dynein light chain 2, cytoplasmic | protein | 86 | 38% helix, 41% strand | Q96FJ2 |
| D | Dynein light chain 2, cytoplasmic | protein | 85 | 39% helix, 36% strand | Q96FJ2 |
| E, F, G, H | Sac-arg-gly-thr-gln-thr-glu | protein | 7 | 0% helix, 57% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.75 | 0.78 | 72 | empty |
Interfaces
12 interfaces between chains.
- A–C · 957 Ų buried · 35 hydrogen bonds · protein-protein
- A–E · 592 Ų buried · 15 hydrogen bonds · protein-protein
- D–H · 573 Ų buried · 17 hydrogen bonds · protein-protein
- C–G · 541 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 536 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (acetylation).
Compared structures
- 2XQQ · Human dynein light chain (DYNLL2) in complex with an in vitro evolved peptide… · the same entry in another collection · chain E against E, TM-score 1.00
- Q96FJ2 · AlphaFold monomer V2.0 prediction for dynein light chain 2, cytoplasmic (Q96FJ2) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q96FJ2
- Elsewhere: RCSB PDB 2XQQ · PDBe 2XQQ · UniProt Q96FJ2
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