SMTL ID : 4dne.1

Crystal structure of a triple-mutant of streptavidin in complex with desthiobiotin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-tetramer

Ligands

4 x DTB: 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID(Non-covalent)

DTB.1: 18 residues within 4Å: Chain A: N.47, L.49, S.51, Y.67, T.69, R.71, G.72, N.73, W.103, A.110, S.112, T.114, W.116, W.132, L.134, D.152 Chain D: W.144 Ligands: SO4.3 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:W.103, A:W.103, A:W.103, A:A.110, A:T.114, A:W.116, A:W.132, A:L.134, D:W.144 Hydrogen bonds: A:N.47, A:S.51, A:T.69, A:T.69, A:N.73, A:S.112, A:S.112, A:D.152 DTB.4: 18 residues within 4Å: Chain B: N.47, L.49, S.51, Y.67, T.69, R.71, G.72, N.73, W.103, A.110, S.112, T.114, W.116, W.132, L.134, D.152 Chain C: W.144 Ligands: SO4.8 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.103, B:W.103, B:W.103, B:A.110, B:T.114, B:W.116, B:W.132, B:L.134, C:W.144 Hydrogen bonds: B:N.47, B:S.51, B:Y.67, B:T.69, B:T.69, B:N.73, B:S.112, B:D.152 DTB.9: 18 residues within 4Å: Chain B: W.144 Chain C: N.47, L.49, S.51, Y.67, T.69, R.71, G.72, N.73, W.103, A.110, S.112, T.114, W.116, W.132, L.134, D.152 Ligands: SO4.11 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.103, C:W.103, C:W.103, C:A.110, C:T.114, C:W.116, C:W.132, C:L.134, B:W.144 Hydrogen bonds: C:N.47, C:S.51, C:Y.67, C:T.69, C:N.73, C:S.112, C:S.112, C:D.152 DTB.12: 18 residues within 4Å: Chain A: W.144 Chain D: N.47, L.49, S.51, Y.67, T.69, R.71, G.72, N.73, W.103, A.110, S.112, T.114, W.116, W.132, L.134, D.152 Ligands: SO4.16 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:W.103, D:W.103, D:W.103, D:A.110, D:T.114, D:W.116, D:W.132, D:L.134, A:W.144 Hydrogen bonds: D:N.47, D:S.51, D:T.69, D:T.69, D:N.73, D:S.112, D:D.152

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.71, G.72 Chain D: N.142, W.144, K.145 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.72 Salt bridges: A:R.71, D:K.145 SO4.3: 4 residues within 4Å: Chain A: G.72 Chain D: W.144, K.145 Ligands: DTB.1 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.145 SO4.5: 3 residues within 4Å: Chain B: A.70, R.71, G.72 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.72, B:G.72 Salt bridges: B:R.71 SO4.6: 5 residues within 4Å: Chain B: G.58, A.59, D.60, G.61, A.62 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.58, B:A.59, B:D.60, B:G.61, B:A.62 SO4.7: 2 residues within 4Å: Chain B: R.71 Chain C: A.141 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.71 SO4.8: 6 residues within 4Å: Chain B: L.134, S.136, L.148 Chain C: W.144, K.145 Ligands: DTB.4 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Salt bridges: C:K.145 Hydrogen bonds: B:S.136 SO4.10: 5 residues within 4Å: Chain B: N.142, W.144, K.145 Chain C: R.71, G.72 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.72 Salt bridges: C:R.71, B:K.145 SO4.11: 4 residues within 4Å: Chain B: W.144, K.145 Chain C: G.72 Ligands: DTB.9 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.145 SO4.13: 3 residues within 4Å: Chain D: A.70, R.71, G.72 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.72, D:G.72 Salt bridges: D:R.71 SO4.14: 5 residues within 4Å: Chain D: G.58, A.59, D.60, G.61, A.62 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.58, D:A.59, D:D.60, D:G.61, D:A.62 SO4.15: 2 residues within 4Å: Chain A: A.141 Chain D: R.71 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.71 SO4.16: 6 residues within 4Å: Chain A: W.144, K.145 Chain D: L.134, S.136, L.148 Ligands: DTB.12 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:S.136 Salt bridges: A:K.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Panwar, P. et al., Contamination from an affinity column: an encounter with a new villain in the world of membrane-protein crystallization. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-09-26

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Streptavidin