SMTL ID : 6mlb.2 (1 other biounit)

Crystal structure of the holo retinal-bound domain-swapped dimer Q108K:K40L:T51F mutant of human cellular retinol binding protein II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: D.91, W.109, I.110 Chain B: T.1 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.1 Water bridges: A:I.110 GOL.5: 3 residues within 4Å: Chain B: V.66, T.87, W.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.88 Water bridges: B:W.88 GOL.6: 6 residues within 4Å: Chain B: D.61, V.62, D.63, D.71, E.72, Y.73 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.63, B:D.63, B:Y.73

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

ACT.2: 7 residues within 4Å: Chain B: V.94, C.95, N.103, G.105, W.106, K.107, T.120 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.107, B:T.120 Hydrogen bonds: B:T.120 ACT.3: 2 residues within 4Å: Chain B: E.89, K.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.89 Salt bridges: B:K.107 ACT.4: 1 residues within 4Å: Chain B: T.37 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.13

1 x RET: RETINAL(Covalent)

RET.7: 11 residues within 4Å: Chain A: F.16, M.20, A.33, Q.38, F.51 Chain B: R.58, L.77, W.106, K.108, L.117, L.119 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:R.58, B:L.77, B:W.106, B:W.106, B:K.108, B:L.117, B:L.119, A:F.16, A:A.33, A:Q.38, A:F.51, A:F.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghanbarpour, A. et al., Engineering the hCRBPII Domain-Swapped Dimer into a New Class of Protein Switches. J.Am.Chem.Soc. (2019)

Release Date

2019-10-16

Peptides

Retinol-binding protein 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Retinol-binding protein 2

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