MolNFT v1 · #181363 · protein
The crystal structure of Q108K:K40E:T53A:R58W:Q38F:Q4F:Y19W mutant of hcrbpii bound with lizfluor chromophore showing excited state intermolecular proton transfer
7LSQ · Retinol-binding protein 2: “The crystal structure of Q108K:K40E:T53A:R58W:Q38F:Q4F:Y19W mutant of hcrbpii bound with lizfluor chromophore…”. X-ray diffraction, 1 ligand (ZFG), 6 pockets (best druggability 0.81). MolNFT v1 #181363 on…
- PDB
- 7LSQ
- 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
- ZFG
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Retinol-binding protein 2 | protein | 133 | 11% helix, 56% strand | P50120 |
Ligands and binding sites
- ZFG · 4-{5-[(2E)-but-2-en-2-yl]thiophen-2-yl}-N,N-dimethylaniline · ligand · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.81 | 0.93 | 38 | ACT, ZFG |
| 2 | 388 | 0.79 | 0.88 | 51 | ACT, ZFG |
| 3 | 438 | 0.78 | 0.86 | 55 | ACT, ZFG |
| 4 | 243 | 0.75 | 0.89 | 31 | ACT |
| 5 | 786 | 0.72 | 0.78 | 86 | empty |
Interfaces
5 interfaces between chains.
- A–B · 477 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 441 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 413 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 405 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 106 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7LSQ · The Crystal Structure of Q108K:K40E:T53A:R58W:Q38F:Q4F:Y19W Mutant of HCRBPII Bound with… · 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 7LSQ · PDBe 7LSQ · UniProt P50120
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