MolNFT v1 · #182070 · protein
The crystal structure of domain-swapped trimer Q108K:K40D:T53A:R58L:Q38F:Q4F mutant of hcrbpii bound with LIZFLUOR3 chromophore showing excited state intermolecular proton transfer
7MFZ · Retinol-binding protein 2: “The crystal structure of domain-swapped trimer Q108K:K40D:T53A:R58L:Q38F:Q4F mutant of hcrbpii bound with…”. X-ray diffraction, 1 ligand (ZFP), 6 pockets (best druggability 0.85). MolNFT v1 #182070 on…
- PDB
- 7MFZ
- Type
- protein
- Length
- 399 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol-binding protein 2
- UniProt
- P50120
- Ligands
- ZFP
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Retinol-binding protein 2 | protein | 133 | 11% helix, 59% strand | P50120 |
Ligands and binding sites
- ZFP · 1-(4-{5-[(2E)-but-2-en-2-yl]thiophen-2-yl}phenyl) azetidine · ligand · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, C
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 | 415 | 0.85 | 0.93 | 50 | ZFP |
| 2 | 427 | 0.83 | 0.91 | 45 | ZFP |
| 3 | 258 | 0.82 | 0.94 | 39 | ACT, ZFP |
| 4 | 152 | 0.42 | 0.74 | 22 | empty |
| 5 | 93 | 0.36 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2068 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2040 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2006 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7MFZ · The Crystal Structure of Domain-Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F Mutant of… · 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 P50120
- Elsewhere: RCSB PDB 7MFZ · PDBe 7MFZ · UniProt P50120
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