SMTL ID : 6wp2.1

The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of HCRBPII

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-trimer

Ligands

6 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1: 5 residues within 4Å: Chain A: H.57 Chain B: H.57 Chain C: H.57 Ligands: ZN.3, ZN.4 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:H.57, B:H.57, C:H.57 ZN.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.3: 5 residues within 4Å: Chain A: H.57 Chain B: H.57 Chain C: H.57 Ligands: ZN.1, ZN.4 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:H.57, B:H.57, C:H.57 ZN.4: 7 residues within 4Å: Chain A: I.32, H.57 Chain B: H.57 Chain C: I.32, H.57 Ligands: ZN.1, ZN.3 No protein-ligand interaction detected (PLIP) ZN.5: 3 residues within 4Å: Chain A: M.10, E.11, S.12 No protein-ligand interaction detected (PLIP) ZN.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: Y.60, E.72, W.106, K.108, L.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.60, A:K.108 GOL.7: 1 residues within 4Å: Chain A: N.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.13 GOL.8: 3 residues within 4Å: Chain B: R.2, Q.44, G.46 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.2, B:Q.44 GOL.9: 7 residues within 4Å: Chain B: M.10, E.11, S.12, N.13, L.36, T.37, L.58 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.10, B:E.11, B:L.36, B:T.37 GOL.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

ACT.12: 5 residues within 4Å: Chain C: M.10, E.11, N.13, T.37, L.58 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.58 Hydrogen bonds: C:T.37

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

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