MolNFT v1 · #126852 · protein
Designed armadillo repeat protein YIIIM5AII in complex with (KR)4-GFP
5MFC: “Designed armadillo repeat protein YIIIM5AII in complex with (KR)4-GFP”. X-ray diffraction, 1 ligand (CRO), 11 pockets (best druggability 0.81). MolNFT v1 #126852 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MFC
- Type
- protein
- Length
- 1,044 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YIIIM5AII; (KR)4-green fluorescent PROTEIN,GREEN fluorescent protein
- UniProt
- A0A059PIQ0
- Ligands
- CRO
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | YIIIM5AII | protein | 285 | 74% helix, 0% strand | — |
| B | (KR)4-green fluorescent PROTEIN,GREEN fluorescent protein | protein | 240 | 10% helix, 49% strand | A0A059PIQ0 |
| C | YIIIM5AII | protein | 282 | 74% helix, 0% strand | — |
| D | (KR)4-green fluorescent PROTEIN,GREEN fluorescent protein | protein | 237 | 11% helix, 49% strand | A0A059PIQ0 |
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 · 2 copies · chains B, D
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.81 | 0.98 | 26 | CRO |
| 2 | 125 | 0.79 | 0.98 | 26 | CRO |
| 3 | 628 | 0.72 | 0.79 | 91 | empty |
| 4 | 219 | 0.56 | 0.79 | 33 | empty |
| 5 | 93 | 0.44 | 0.80 | 15 | ACT |
Interfaces
5 interfaces between chains.
- C–D · 1889 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 1798 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 273 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 192 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 161 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 5MFC · Designed armadillo repeat protein YIIIM5AII in complex with (KR)4-GFP · 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
- Every structure of UniProt A0A059PIQ0
- Elsewhere: RCSB PDB 5MFC · PDBe 5MFC · UniProt A0A059PIQ0
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