SMTL ID : 3wyq.1

Crystal structure of the low-immunogenic core streptavidin mutant LISA-314 (Y22S/Y83S/R84K/E101D/R103K/E116N) at 1.0 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.00 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.6 12 PLIP interactions: 12 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 BTN.9: 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.13 13 PLIP interactions: 13 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 BTN.14: 19 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, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Ligands: GOL.19 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:A.38, 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.22: 19 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, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Ligands: GOL.26 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:A.38, 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

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: Q.83, N.93, T.94, Q.95 Chain B: A.107, S.110, T.111 Chain C: H.115 Ligands: GOL.18 Ligand excluded by PLIP GOL.3: 4 residues within 4Å: Chain A: L.13, A.34, V.35 Chain D: A.105 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: G.22, A.23, D.24, A.26 Ligands: SO4.8 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: Q.12, L.13, G.114, H.115 Chain D: W.108 Ligands: GOL.15 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: N.37, S.100, L.112 Chain D: W.108 Ligands: BTN.1 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: E.2, G.4, Y.84, G.86, G.87 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain B: S.57, G.58, T.59, Y.84, V.85, G.86 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain B: Q.12, L.13, W.96, G.114, H.115, D.116 Chain C: W.108 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: S.57 Chain B: G.101, T.102, T.103, N.106, K.109 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain B: L.112 Chain C: W.108, K.109 Ligands: BTN.9 Ligand excluded by PLIP GOL.15: 9 residues within 4Å: Chain A: H.115 Chain C: Q.83, N.93, T.94, Q.95 Chain D: A.107, S.110, T.111 Ligands: GOL.5 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain B: A.105 Chain C: L.13, A.34, V.35 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain C: G.22, A.23, D.24, A.26 Ligands: SO4.21 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain B: W.108 Chain C: Q.12, L.13, G.114, H.115 Ligands: GOL.2 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain B: W.108 Chain C: N.37, S.100, L.112 Ligands: BTN.14 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain C: E.2, G.4, Y.84, G.86, G.87 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain D: S.57, G.58, T.59, Y.84, V.85, G.86 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain A: W.108 Chain D: Q.12, L.13, W.96, G.114, H.115, D.116 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain C: S.57 Chain D: G.101, T.102, T.103, N.106, K.109 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain A: W.108, K.109 Chain D: L.112 Ligands: BTN.22 Ligand excluded by PLIP

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

SO4.8: 4 residues within 4Å: Chain A: A.1, G.22, A.23 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.1, A:A.23 SO4.21: 4 residues within 4Å: Chain C: A.1, G.22, A.23 Ligands: GOL.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.1, C:A.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawato, T. et al., Crystal structure of streptavidin mutant with low immunogenicity. J.Biosci.Bioeng. (2015)

Release Date

2014-12-24

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Streptavidin