SMTL ID : 2zsc.1

Tamavidin2, Novel Avidin-like Biotin-Binding Proteins from an Edible Mushroom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-tetramer

Ligands

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: S.2, V.4, P.55, V.61, F.84, F.85, S.86 Ligands: GOL.3 Ligand excluded by PLIP GOL.2: 4 residues within 4Å: Chain A: D.27, T.29, R.50 Chain C: P.46 Ligand excluded by PLIP GOL.3: 6 residues within 4Å: Chain A: G.58, Q.59, F.85, S.86, E.87 Ligands: GOL.1 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: Y.42, N.71, S.72, K.73 Ligands: MG.6 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain B: S.2, V.4, P.55, V.61, F.84, F.85, S.86 Ligands: GOL.9 Ligand excluded by PLIP GOL.8: 2 residues within 4Å: Chain B: R.104, G.105 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain B: P.56, G.58, Q.59, F.85, S.86, E.87 Ligands: GOL.7 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain B: D.27, T.29, R.50 Chain D: P.46 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain B: Y.13, N.14, E.15, S.117, T.119 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain C: S.2, V.4, P.55, V.61, F.84, F.85, S.86 Ligands: GOL.17 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain A: P.46 Chain C: D.27, T.29, R.50 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain C: G.58, Q.59, F.85, S.86, E.87 Ligands: GOL.15 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain C: Y.42, N.71, S.72, K.73 Ligands: MG.20 Ligand excluded by PLIP GOL.21: 8 residues within 4Å: Chain D: S.2, V.4, P.55, V.61, F.84, F.85, S.86 Ligands: GOL.23 Ligand excluded by PLIP GOL.22: 2 residues within 4Å: Chain D: R.104, G.105 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain D: P.56, G.58, Q.59, F.85, S.86, E.87 Ligands: GOL.21 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain B: P.46 Chain D: D.27, T.29, R.50 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain D: Y.13, N.14, E.15, S.117, T.119 Ligand excluded by PLIP

4 x BTN: BIOTIN(Non-covalent)

BTN.5: 16 residues within 4Å: Chain A: N.14, L.16, S.18, Y.34, S.36, V.38, V.41, W.69, I.74, S.76, T.78, W.80, W.96, L.98, D.116 Chain B: W.108 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.41, A:W.69, A:W.69, A:W.69, A:L.98 Hydrogen bonds: A:N.14, A:S.18, A:Y.34, A:S.36, A:S.76, A:D.116 Water bridges: A:D.40 BTN.13: 16 residues within 4Å: Chain A: W.108 Chain B: N.14, L.16, S.18, Y.34, S.36, V.38, V.41, W.69, I.74, S.76, T.78, W.80, W.96, L.98, D.116 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.41, B:W.69, B:W.69, B:W.69, B:L.98 Hydrogen bonds: B:N.14, B:S.18, B:Y.34, B:S.36, B:S.76, B:D.116 Water bridges: B:D.40 BTN.19: 16 residues within 4Å: Chain C: N.14, L.16, S.18, Y.34, S.36, V.38, V.41, W.69, I.74, S.76, T.78, W.80, W.96, L.98, D.116 Chain D: W.108 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:V.41, C:W.69, C:W.69, C:W.69, C:L.98 Hydrogen bonds: C:N.14, C:S.18, C:S.36, C:S.76, C:D.116 Water bridges: C:D.40 BTN.27: 16 residues within 4Å: Chain C: W.108 Chain D: N.14, L.16, S.18, Y.34, S.36, V.38, V.41, W.69, I.74, S.76, T.78, W.80, W.96, L.98, D.116 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:V.41, D:W.69, D:W.69, D:W.69, D:L.98 Hydrogen bonds: D:N.14, D:S.18, D:S.36, D:S.76, D:D.116 Water bridges: D:D.40

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.6: 6 residues within 4Å: Chain A: V.41, Y.42, V.43, Y.45, N.71 Ligands: GOL.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.45, H2O.6 MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain B: V.41, Y.42, Y.45, N.71 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:Y.45 MG.20: 6 residues within 4Å: Chain C: V.41, Y.42, V.43, Y.45, N.71 Ligands: GOL.18 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:Y.45, H2O.24 MG.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain D: V.41, Y.42, Y.45, N.71 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:Y.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takakura, Y. et al., Tamavidins--novel avidin-like biotin-binding proteins from the Tamogitake mushroom. Febs J. (2009)

Release Date

2009-02-17

Peptides

Tamavidin2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Tamavidin2