Research workbench
Crystal structure of darpin-darpin rigid fusion, variant DD_OFF7_10_3G124 in complex with maltose-binding protein and green fluorescent protein
Analyse Crystal structure of darpin-darpin rigid fusion, variant DD_OFF7_10_3G124 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LEL
- Type
- protein
- Length
- 2,718 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DD_OFF7_10_3G124; Maltose-binding periplasmic protein; Green fluorescent protein
- UniProt
- P0AEY0, P42212
- Ligands
- CRO
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DD_OFF7_10_3G124 | protein | 313 | 56% helix, 0% strand | — |
| B | Maltose-binding periplasmic protein | protein | 368 | 46% helix, 20% strand | P0AEY0 |
| C, F, I | Green fluorescent protein | protein | 226 | 11% helix, 52% strand | P42212 |
| E | Maltose-binding periplasmic protein | protein | 369 | 46% helix, 19% strand | P0AEY0 |
| G | DD_OFF7_10_3G124 | protein | 311 | 56% helix, 0% strand | — |
| H | Maltose-binding periplasmic protein | protein | 366 | 45% helix, 20% strand | P0AEY0 |
Ligands and binding sites
- CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 3 copies · chains C, F, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.79 | 0.97 | 26 | CRO |
| 2 | 99 | 0.79 | 0.99 | 25 | CRO |
| 3 | 939 | 0.79 | 0.81 | 106 | empty |
| 4 | 900 | 0.79 | 0.81 | 112 | empty |
| 5 | 94 | 0.78 | 0.99 | 26 | CRO |
Interfaces
17 interfaces between chains.
- G–I · 1151 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1098 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1090 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 732 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 705 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (chromophore).
Compared structures
- 5LEL · Crystal structure of DARPin-DARPin rigid fusion, variant DD_Off7_10_3G124 in complex with… · the same entry in another collection · chain I against I, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 P0AEY0
- Every structure of UniProt P42212
- Elsewhere: RCSB PDB 5LEL · PDBe 5LEL · UniProt P0AEY0 · UniProt P42212
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