MolNFT v1 · #182068 · protein
The crystal structure of Q108K:K40H:T53A:R58L:Q38F:Q4F mutant of hcrbpii bound with FR1 chromophore showing excited state intermolecular proton transfer
7MFX · Retinol-binding protein 2: “The crystal structure of Q108K:K40H:T53A:R58L:Q38F:Q4F mutant of hcrbpii bound with FR1 chromophore showing…”. X-ray diffraction, 1 ligand (ZFJ), 10 pockets (best druggability 0.86). MolNFT v1 #182068 on…
- PDB
- 7MFX
- Type
- protein
- Length
- 532 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol-binding protein 2
- UniProt
- P50120
- Ligands
- ZFJ
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Retinol-binding protein 2 | protein | 133 | 12% helix, 56% strand | P50120 |
Ligands and binding sites
- ZFJ · (4aP)-N,N-diethyl-9,9-dimethyl-7-[(1E)-prop-1-en-1-yl]-9H-fluoren-2-amine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 584 | 0.86 | 0.91 | 60 | ZFJ |
| 2 | 271 | 0.83 | 0.94 | 35 | ZFJ |
| 3 | 277 | 0.82 | 0.93 | 36 | ZFJ |
| 4 | 245 | 0.82 | 0.94 | 33 | ZFJ |
| 5 | 234 | 0.70 | 0.86 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–D · 611 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 470 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 453 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 447 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 305 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7MFX · The Crystal Structure of Q108K:K40H:T53A:R58L:Q38F:Q4F Mutant of HCRBPII Bound with FR1… · the same entry in another collection · chain D against D, 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 P50120
- Elsewhere: RCSB PDB 7MFX · PDBe 7MFX · UniProt P50120
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