SMTL ID : 6wnj.1

The Crystal Structure of Apo Domain-Swapped Trimer Q108K:T51D:A28C:I32C of HCRBPII

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: K.107, E.118 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.107 GOL.2: 6 residues within 4Å: Chain A: D.91, V.92, W.109, I.110, E.111 Chain B: T.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.91, A:E.111 GOL.3: 2 residues within 4Å: Chain A: E.89, K.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.89, A:K.107 GOL.7: 6 residues within 4Å: Chain A: Y.60, V.62, K.108 Chain B: K.40, D.51, T.53 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.40, B:K.40, B:D.51, B:T.53, A:Y.60, A:K.108 GOL.8: 2 residues within 4Å: Chain C: W.109, E.118 No protein-ligand interaction detected (PLIP) GOL.9: 4 residues within 4Å: Chain C: K.21, F.27, R.30, K.31 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.21, C:K.21, C:R.30, C:R.30, C:K.31 GOL.10: 7 residues within 4Å: Chain B: Y.60, V.62, F.64, K.108 Chain C: K.40, D.51, T.53 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.40, C:D.51, C:D.51, C:T.53, C:T.53, B:K.108

3 x 144: TRIS-HYDROXYMETHYL-METHYL-AMMONIUM(Non-covalent)

144.4: 3 residues within 4Å: Chain A: N.59, D.61 Chain B: K.52 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.52, A:D.61 Salt bridges: A:D.61 144.11: 10 residues within 4Å: Chain A: T.53 Chain C: Y.60, D.61, V.62, E.72, Y.73, T.74, K.75, S.76 Ligands: 144.12 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Water bridges: A:T.53, C:Y.60 Hydrogen bonds: C:S.76 Salt bridges: C:E.72 144.12: 7 residues within 4Å: Chain A: D.51 Chain C: V.62, E.72, Q.97, W.106, K.108 Ligands: 144.11 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.97, C:K.108, C:K.108, A:D.51 Water bridges: C:Q.97 Salt bridges: C:E.72

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 5 residues within 4Å: Chain A: D.61, V.62, D.71, E.72, Y.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.61, A:D.71, A:Y.73 SO4.6: 2 residues within 4Å: Chain A: K.101 Chain B: A.22 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.101 Hydrogen bonds: B:A.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghanbarpour, A. et al., Human Cellular Retinol Binding Protein II Forms a Domain-Swapped Trimer Representing a Novel Fold and a New Template for Protein Engineering. Chembiochem (2020)

Release Date

2020-08-19

Peptides

Retinol-binding protein 2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Retinol-binding protein 2