SMTL ID : 8d6n.1

Q108K:K40L:T53A:R58L:Q38F:Q4F mutant of hCRBPII bound to synthetic fluorophore CM1V

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

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

ACT.1: 7 residues within 4Å: Chain A: Y.60, V.62, E.72, C.95, Q.97, W.106 Ligands: GOL.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.62 Hydrogen bonds: A:Y.60, A:Q.97, A:W.106 ACT.4: 1 residues within 4Å: Chain A: D.61 No protein-ligand interaction detected (PLIP) ACT.6: 3 residues within 4Å: Chain A: T.65, V.68 Ligands: GOL.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.65

1 x RH6: (2E)-3-[7-(diethylamino)-2-oxo-2H-1-benzopyran-3-yl]prop-2-enal, bound form(Covalent)

RH6.2: 15 residues within 4Å: Chain A: F.16, M.20, A.33, F.38, L.40, A.53, S.55, L.58, N.59, Y.60, L.77, W.106, K.108, L.117, L.119 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.16, A:A.33, A:F.38, A:L.58, A:Y.60, A:Y.60, A:Y.60, A:W.106, A:K.108, A:L.117, A:L.117 pi-Stacking: A:Y.60

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: D.61, D.63, K.75 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.63, A:D.63, A:K.75, A:K.75 GOL.5: 6 residues within 4Å: Chain A: V.68, E.69, F.70, D.71 Ligands: ACT.6, MLA.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.71 GOL.7: 4 residues within 4Å: Chain A: L.85, T.87, E.89, V.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.87, A:E.89 GOL.8: 2 residues within 4Å: Chain A: S.12, V.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.12 GOL.9: 5 residues within 4Å: Chain A: K.21, A.22, D.123, Q.124 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.21, A:D.123 GOL.10: 6 residues within 4Å: Chain A: A.22, K.101, E.102, C.121, G.122 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.102, A:C.121 GOL.13: 10 residues within 4Å: Chain A: N.59, Y.60, D.61, V.62, E.72, Y.73, T.74, S.76, L.77 Ligands: ACT.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.59, A:D.61, A:E.72, A:Y.73

2 x MLA: MALONIC ACID(Non-covalent)

MLA.11: 2 residues within 4Å: Chain A: E.100, K.101 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.100 MLA.12: 4 residues within 4Å: Chain A: D.63, F.64, F.70 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.70 Water bridges: A:D.63, A:T.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maity, S. et al., Light controlled reversible Michael addition of cysteine: a new tool for dynamic site-specific labeling of proteins. Analyst (2023)

Release Date

2023-02-01

Peptides

Retinol-binding protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Retinol-binding protein 2