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

Crystal structure of Retinal-bound holo Q108K:K40L:T51W domain-swapped dimer of human cellular retinol binding protein 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-dimer

Ligands

2 x RET: RETINAL(Covalent)

RET.1: 15 residues within 4Å: Chain A: F.57, S.76, L.77, W.106, K.108, L.117, L.119 Chain B: F.16, Y.19, M.20, I.25, A.33, W.51, T.53, S.55 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.16, B:Y.19, B:I.25, B:A.33, B:W.51, B:W.51, B:T.53, A:F.57, A:W.106, A:W.106, A:K.108, A:L.117, A:L.117, A:L.119 RET.5: 15 residues within 4Å: Chain A: F.16, A.33, Q.38, W.51, T.53, S.55 Chain B: F.57, R.58, L.77, W.106, K.108, L.117, L.119, Q.128 Ligands: ACT.9 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.57, B:L.77, B:W.106, B:W.106, B:K.108, B:L.117, B:L.117, B:L.119, A:F.16, A:A.33, A:Q.38, A:W.51, A:W.51, A:W.51, A:T.53

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

ACT.2: 5 residues within 4Å: Chain A: N.5, G.6, V.41, I.42, D.43 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.43 Hydrogen bonds: A:N.5, A:G.6 ACT.3: 5 residues within 4Å: Chain A: D.91, V.92, W.109, I.110 Chain B: T.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.110 ACT.6: 5 residues within 4Å: Chain B: Y.60, D.61, V.62, E.72, Y.73 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.60 Hydrogen bonds: B:D.61, B:Y.73 ACT.7: 3 residues within 4Å: Chain A: W.88 Chain B: R.2, D.47 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.47 Salt bridges: B:R.2 ACT.8: 4 residues within 4Å: Chain B: M.10, E.11, S.12, T.37 No protein-ligand interaction detected (PLIP) ACT.9: 8 residues within 4Å: Chain A: Y.19 Chain B: Y.60, E.72, L.77, Q.97, R.104, W.106 Ligands: RET.5 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.60, B:L.77 Hydrogen bonds: B:Q.97, A:Y.19 Salt bridges: B:R.104

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: R.127, V.129 Chain B: S.12, E.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.14 GOL.10: 5 residues within 4Å: Chain B: R.2, D.3, Q.44, D.45, G.46 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.2, B:Q.44, B:G.46

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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