SMTL ID : 3mg5.1

Core-streptavidin mutant F130L in complex with biotin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-tetramer

Ligands

4 x BTN: BIOTIN(Non-covalent)

BTN.1: 19 residues within 4Å: Chain A: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Chain D: W.108 Ligands: GOL.14 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.38, A:W.67, A:W.67, A:W.67, A:L.98 Hydrogen bonds: A:N.11, A:S.15, A:S.33, A:N.37, A:S.76, A:S.76, A:D.116 Water bridges: A:N.37 BTN.4: 19 residues within 4Å: Chain B: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Chain C: W.108 Ligands: GOL.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.38, B:W.67, B:W.67, B:W.67, B:L.98 Hydrogen bonds: B:N.11, B:S.15, B:Y.31, B:S.33, B:N.37, B:S.76, B:S.76, B:D.116 Water bridges: B:N.37, B:N.37 BTN.8: 18 residues within 4Å: Chain B: W.108 Chain C: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Ligands: GOL.10 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.67, C:W.67, C:W.67, C:L.98 Hydrogen bonds: C:N.11, C:S.15, C:Y.31, C:S.33, C:N.37, C:S.76, C:S.76, C:D.116 BTN.12: 18 residues within 4Å: Chain A: W.108 Chain D: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Ligands: GOL.15 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.67, D:W.67, D:W.67, D:L.98 Hydrogen bonds: D:N.11, D:S.15, D:S.33, D:N.37, D:S.76, D:S.76, D:D.116

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: Q.12, L.13, G.114, H.115 Chain D: W.108 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain A Water bridges: D:A.107, D:W.108, A:H.115, A:H.115, A:H.115 Hydrogen bonds: A:Q.12, A:H.115 GOL.3: 3 residues within 4Å: Chain A: G.4, I.5, Y.84 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.4, A:I.5, A:Y.84 Water bridges: A:G.4, A:T.6 GOL.5: 5 residues within 4Å: Chain B: Q.12, L.13, G.114, H.115 Chain C: W.108 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.12, B:H.115 Water bridges: B:H.115 GOL.6: 6 residues within 4Å: Chain B: N.37, L.98, S.100, L.112 Chain C: W.108 Ligands: BTN.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.37, B:S.100 Water bridges: B:N.37 GOL.7: 7 residues within 4Å: Chain A: D.24, R.47, S.50 Chain B: V.43, K.68, N.69, N.70 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.68, B:K.68, A:S.50, A:S.50 Water bridges: A:R.47 GOL.9: 6 residues within 4Å: Chain B: A.107, W.108 Chain C: Q.12, L.13, G.114, H.115 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Water bridges: B:A.107, B:W.108 Hydrogen bonds: C:Q.12, C:H.115 GOL.10: 4 residues within 4Å: Chain B: W.108, K.109 Chain C: L.112 Ligands: BTN.8 1 PLIP interactions: 1 interactions with chain C Water bridges: C:S.100 GOL.11: 5 residues within 4Å: Chain C: G.14, S.15, T.16, E.32, A.34 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.16 GOL.13: 7 residues within 4Å: Chain A: W.108 Chain D: Q.12, L.13, W.96, G.114, H.115, D.116 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.12, D:H.115 Water bridges: D:H.115 GOL.14: 5 residues within 4Å: Chain A: G.36, S.100, L.112 Chain D: W.108 Ligands: BTN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.37, A:S.100, A:S.100 Water bridges: A:S.76 GOL.15: 6 residues within 4Å: Chain A: W.108 Chain D: N.37, L.98, S.100, L.112 Ligands: BTN.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.37 Water bridges: D:L.98, D:S.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., A distal point mutation in the streptavidin-biotin complex preserves structure but diminishes binding affinity: experimental evidence of electronic polarization effects?. Biochemistry (2010)

Release Date

2010-05-26

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Streptavidin