MolNFT v1 · #63069 · protein
New crystal structure of human tear lipocalin in complex with 1,4- butanediol in space group P21
3EYC · Lipocalin-1: “New crystal structure of human tear lipocalin in complex with 1,4- butanediol in space group P21”. X-ray diffraction, 6 pockets (best druggability 0.85). MolNFT v1 #63069 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3EYC
- Type
- protein
- Length
- 557 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipocalin-1
- UniProt
- P31025
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipocalin-1 | protein | 143 | 9% helix, 52% strand | P31025 |
| B | Lipocalin-1 | protein | 140 | 9% helix, 54% strand | P31025 |
| C | Lipocalin-1 | protein | 137 | 9% helix, 51% strand | P31025 |
| D | Lipocalin-1 | protein | 137 | 9% helix, 53% strand | P31025 |
Ligands and binding sites
- BU1 · 1,4-butanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.85 | 0.86 | 98 | BU1 |
| 2 | 556 | 0.79 | 0.85 | 52 | BU1 |
| 3 | 491 | 0.72 | 0.81 | 47 | BU1 |
| 4 | 70 | 0.41 | 0.80 | 20 | empty |
| 5 | 59 | 0.36 | 0.78 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–C · 885 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 206 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 175 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3EYC · New crystal structure of human tear lipocalin in complex with 1,4-butanediol in space… · the same entry in another collection · chain D against D, TM-score 1.00
- P31025 · AlphaFold monomer V2.0 prediction for lipocalin-1 (P31025) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P31025
- Elsewhere: RCSB PDB 3EYC · PDBe 3EYC · UniProt P31025
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