Research workbench
Crystal structure of auxin-binding protein 1 in complex with 1- naphthalene acetic acid
Analyse Crystal structure of auxin-binding protein 1 in complex with 1- naphthalene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LRH
- Type
- protein
- Length
- 640 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Auxin-binding protein 1
- UniProt
- P13689
- Ligands
- NLA, MAN, NAG, BMA, ZN
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Auxin-binding protein 1 | protein | 160 | 11% helix, 41% strand | P13689 |
Ligands and binding sites
- NLA · Naphthalen-1-yl-acetic acid · ligand · 4 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains D, C, B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, D, B, C
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains D, C, B, A
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.73 | 0.92 | 27 | NLA |
| 2 | 123 | 0.72 | 0.92 | 28 | NLA |
| 3 | 92 | 0.71 | 0.93 | 24 | NLA |
| 4 | 111 | 0.71 | 0.92 | 24 | NLA |
| 5 | 77 | 0.49 | 0.84 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1485 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1468 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 376 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1LRH · Crystal structure of auxin-binding protein 1 in complex with 1-naphthalene acetic acid · the same entry in another collection · chain A against A, TM-score 1.00
- P13689 · AlphaFold monomer V2.0 prediction for auxin-binding protein 1 (P13689) · a predicted model of the same protein · 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 P13689
- Elsewhere: RCSB PDB 1LRH · PDBe 1LRH · UniProt P13689
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