SMTL ID : 7mfz.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-trimer

Ligands

3 x ZFP: 1-(4-{5-[(2E)-but-2-en-2-yl]thiophen-2-yl}phenyl)azetidine(Covalent)

ZFP.1: 5 residues within 4Å: Chain A: Y.60, W.106, K.108, L.117 Chain B: A.53 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.53, A:W.106, A:K.108, A:L.117 ZFP.3: 9 residues within 4Å: Chain B: R.35, S.76, L.77, K.108, L.117, L.119 Chain C: F.16, F.38, D.40 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.77, B:K.108, B:L.117, B:L.119, C:F.16 pi-Stacking: C:F.38 ZFP.7: 13 residues within 4Å: Chain A: F.16, M.20, A.33, F.38, D.40 Chain C: Y.60, S.76, L.77, W.106, K.108, L.117, L.119 Ligands: ACT.4 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:F.16, A:F.38, C:Y.60, C:L.77, C:W.106, C:K.108, C:L.117, C:L.119

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.4: 7 residues within 4Å: Chain A: Y.19 Chain C: Y.60, T.74, L.77, Q.97, R.104 Ligands: ZFP.7 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:T.74, C:L.77 Hydrogen bonds: C:Y.60, C:Q.97, A:Y.19

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: D.24 Chain C: E.100, K.101 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.100, C:E.100, C:K.101 GOL.6: 3 residues within 4Å: Chain C: R.80, H.81, E.100 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.81, C:E.100 Water bridges: C:E.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Santos, E.M. et al., Design of Large Stokes Shift Fluorescent Proteins Based on Excited State Proton Transfer of an Engineered Photobase. J.Am.Chem.Soc. (2021)

Release Date

2022-01-12

Peptides

Retinol-binding protein 2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Retinol-binding protein 2

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