SMTL ID : 4bcs.1

Crystal structure of an avidin mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

ACT.1: 4 residues within 4Å: Chain A: T.11, Q.121, R.122, T.123 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.121, A:R.122 Hydrogen bonds: A:T.11, A:R.122 Salt bridges: A:R.122 ACT.7: 4 residues within 4Å: Chain C: T.11, Q.121, R.122, T.123 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Q.121, C:R.122 Hydrogen bonds: C:T.11, C:R.122 Salt bridges: C:R.122

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: T.11, D.12, D.13, I.117, T.119 No protein-ligand interaction detected (PLIP) PEG.8: 5 residues within 4Å: Chain C: T.11, D.12, D.13, I.117, T.119 No protein-ligand interaction detected (PLIP)

4 x BTN: BIOTIN(Non-covalent)

BTN.3: 17 residues within 4Å: Chain A: D.12, L.14, S.16, Y.33, T.35, V.37, A.38, D.39, W.68, F.70, S.71, S.73, T.75, F.77, W.95, N.116 Chain D: W.108 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.68, A:W.68, A:F.70 Hydrogen bonds: A:S.16, A:Y.33, A:T.35, A:D.39, A:S.71, A:S.73, A:N.116, A:N.116 Water bridges: A:D.39, A:N.40 BTN.6: 16 residues within 4Å: Chain B: D.12, L.14, S.16, Y.33, T.35, V.37, A.38, D.39, W.68, F.70, S.71, S.73, T.75, W.95, N.116 Chain C: W.108 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.68, B:W.68, B:W.68, B:F.70 Hydrogen bonds: B:S.16, B:T.35, B:T.35, B:D.39, B:S.71, B:S.73, B:N.116, B:N.116 Water bridges: B:N.40 BTN.9: 17 residues within 4Å: Chain B: W.108 Chain C: D.12, L.14, S.16, Y.33, T.35, V.37, A.38, D.39, W.68, F.70, S.71, S.73, T.75, F.77, W.95, N.116 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.68, C:W.68, C:F.70 Hydrogen bonds: C:S.16, C:Y.33, C:T.35, C:D.39, C:S.71, C:S.73, C:N.116, C:N.116 Water bridges: C:D.39, C:N.40 BTN.12: 16 residues within 4Å: Chain A: W.108 Chain D: D.12, L.14, S.16, Y.33, T.35, V.37, A.38, D.39, W.68, F.70, S.71, S.73, T.75, W.95, N.116 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:W.68, D:W.68, D:W.68, D:F.70 Hydrogen bonds: D:S.16, D:T.35, D:T.35, D:D.39, D:S.71, D:S.73, D:N.116, D:N.116 Water bridges: D:N.40

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 5 residues within 4Å: Chain A: E.72 Chain C: H.54, K.55, R.56, A.57 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:K.55, C:R.56, C:A.57, A:E.72, A:E.72 Water bridges: C:H.54 Salt bridges: C:H.54, C:R.56 PO4.5: 5 residues within 4Å: Chain B: H.54, K.55, R.56, A.57 Chain D: E.72 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.55, B:R.56, B:A.57 Salt bridges: B:H.54, B:R.56 PO4.10: 5 residues within 4Å: Chain A: H.54, K.55, R.56, A.57 Chain C: E.72 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:K.55, A:R.56, A:A.57, C:E.72, C:E.72 Water bridges: A:H.54 Salt bridges: A:H.54, A:R.56 PO4.11: 5 residues within 4Å: Chain B: E.72 Chain D: H.54, K.55, R.56, A.57 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.55, D:R.56, D:A.57 Salt bridges: D:H.54, D:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taskinen, B. et al., A Novel Chimeric Avidin with Increased Thermal Stability Using DNA Shuffling. Plos One (2014)

Release Date

2013-10-16

Peptides

CHIMERIC AVIDIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

CHIMERIC AVIDIN