SMTL ID : 4irw.1

Co-crystallization of streptavidin-biotin complex with a lanthanide-ligand complex gives rise to a novel crystal form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

48 x PDC: PYRIDINE-2,6-DICARBOXYLIC ACID(Non-covalent)(Non-functional Binders)

PDC.1: 6 residues within 4Å: Chain A: H.77 Chain B: A.55, T.56 Ligands: PDC.4, PDC.8, TB.16 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.75 Salt bridges: A:H.77 PDC.2: 4 residues within 4Å: Chain A: R.43 Ligands: PDC.6, PDC.7, TB.15 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.43 PDC.3: 8 residues within 4Å: Chain A: G.38, N.39, R.74 Chain C: W.110, K.111 Ligands: PDC.9, PDC.10, TB.18 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:N.39 Hydrogen bonds: A:G.38 Salt bridges: C:K.111 PDC.4: 10 residues within 4Å: Chain A: K.70, N.71, N.72, Y.73, R.74, N.75 Chain B: A.53 Ligands: PDC.1, PDC.8, TB.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.75 Salt bridges: A:H.77 PDC.5: 5 residues within 4Å: Chain A: E.34, E.41, S.42 Ligands: PDC.6, TB.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.42 PDC.6: 7 residues within 4Å: Chain A: E.41, S.42, R.43, Y.73 Ligands: PDC.2, PDC.5, TB.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.73 Water bridges: A:R.43, A:R.43 Salt bridges: A:R.43 PDC.7: 2 residues within 4Å: Ligands: PDC.2, TB.15 No protein-ligand interaction detected (PLIP) PDC.8: 5 residues within 4Å: Chain A: R.74, N.75 Ligands: PDC.1, PDC.4, TB.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.75 PDC.9: 5 residues within 4Å: Chain C: K.111 Ligands: PDC.3, PDC.10, TB.18, PDC.47 3 PLIP interactions: 3 interactions with chain C Water bridges: C:K.111, C:K.111 Salt bridges: C:K.111 PDC.10: 11 residues within 4Å: Chain A: N.39, A.76, S.78, L.100, S.102, L.114 Chain C: K.111 Ligands: PDC.3, PDC.9, BTN.13, TB.18 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.114 Salt bridges: C:K.111 PDC.11: 5 residues within 4Å: Chain A: D.26, R.49 Chain B: V.45 Ligands: PDC.12, TB.17 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:V.45, A:R.49 Hydrophobic interactions: A:D.26 Salt bridges: A:R.49 PDC.12: 9 residues within 4Å: Chain A: A.28, R.49 Chain B: T.30, G.31, V.45, L.46, T.47 Ligands: PDC.11, TB.17 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.45 Salt bridges: A:R.49 PDC.20: 6 residues within 4Å: Chain A: A.55, T.56 Chain B: H.77 Ligands: PDC.23, PDC.27, TB.35 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.75 Salt bridges: B:H.77 PDC.21: 4 residues within 4Å: Chain B: R.43 Ligands: PDC.25, PDC.26, TB.34 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.43 PDC.22: 8 residues within 4Å: Chain B: G.38, N.39, R.74 Chain D: W.110, K.111 Ligands: PDC.28, PDC.29, TB.37 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:N.39 Hydrogen bonds: B:G.38 Salt bridges: D:K.111 PDC.23: 10 residues within 4Å: Chain A: A.53 Chain B: K.70, N.71, N.72, Y.73, R.74, N.75 Ligands: PDC.20, PDC.27, TB.35 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.75 Salt bridges: B:H.77 PDC.24: 5 residues within 4Å: Chain B: E.34, E.41, S.42 Ligands: PDC.25, TB.33 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.42 PDC.25: 7 residues within 4Å: Chain B: E.41, S.42, R.43, Y.73 Ligands: PDC.21, PDC.24, TB.33 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.73 Water bridges: B:R.43, B:R.43 Salt bridges: B:R.43 PDC.26: 2 residues within 4Å: Ligands: PDC.21, TB.34 No protein-ligand interaction detected (PLIP) PDC.27: 5 residues within 4Å: Chain B: R.74, N.75 Ligands: PDC.20, PDC.23, TB.35 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.75 PDC.28: 5 residues within 4Å: Chain D: K.111 Ligands: PDC.22, PDC.29, TB.37, PDC.66 3 PLIP interactions: 3 interactions with chain D Water bridges: D:K.111, D:K.111 Salt bridges: D:K.111 PDC.29: 11 residues within 4Å: Chain B: N.39, A.76, S.78, L.100, S.102, L.114 Chain D: K.111 Ligands: PDC.22, PDC.28, BTN.32, TB.37 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Salt bridges: D:K.111 Hydrophobic interactions: B:L.114 PDC.30: 5 residues within 4Å: Chain A: V.45 Chain B: D.26, R.49 Ligands: PDC.31, TB.36 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:V.45, B:R.49 Hydrophobic interactions: B:D.26 Salt bridges: B:R.49 PDC.31: 9 residues within 4Å: Chain A: T.30, G.31, V.45, L.46, T.47 Chain B: A.28, R.49 Ligands: PDC.30, TB.36 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.45 Salt bridges: B:R.49 PDC.39: 6 residues within 4Å: Chain C: H.77 Chain D: A.55, T.56 Ligands: PDC.42, PDC.46, TB.54 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.75 Salt bridges: C:H.77 PDC.40: 4 residues within 4Å: Chain C: R.43 Ligands: PDC.44, PDC.45, TB.53 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.43 PDC.41: 8 residues within 4Å: Chain A: W.110, K.111 Chain C: G.38, N.39, R.74 Ligands: PDC.47, PDC.48, TB.56 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:N.39 Hydrogen bonds: C:G.38 Salt bridges: A:K.111 PDC.42: 10 residues within 4Å: Chain C: K.70, N.71, N.72, Y.73, R.74, N.75 Chain D: A.53 Ligands: PDC.39, PDC.46, TB.54 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.75 Salt bridges: C:H.77 PDC.43: 5 residues within 4Å: Chain C: E.34, E.41, S.42 Ligands: PDC.44, TB.52 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.34, C:S.42 PDC.44: 7 residues within 4Å: Chain C: E.41, S.42, R.43, Y.73 Ligands: PDC.40, PDC.43, TB.52 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.73 Water bridges: C:R.43, C:R.43 Salt bridges: C:R.43 PDC.45: 2 residues within 4Å: Ligands: PDC.40, TB.53 No protein-ligand interaction detected (PLIP) PDC.46: 5 residues within 4Å: Chain C: R.74, N.75 Ligands: PDC.39, PDC.42, TB.54 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.75 PDC.47: 5 residues within 4Å: Chain A: K.111 Ligands: PDC.9, PDC.41, PDC.48, TB.56 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.111, A:K.111 Salt bridges: A:K.111 PDC.48: 11 residues within 4Å: Chain A: K.111 Chain C: N.39, A.76, S.78, L.100, S.102, L.114 Ligands: PDC.41, PDC.47, BTN.51, TB.56 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Salt bridges: A:K.111 Hydrophobic interactions: C:L.114 PDC.49: 5 residues within 4Å: Chain C: D.26, R.49 Chain D: V.45 Ligands: PDC.50, TB.55 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:D.26 Water bridges: C:R.49, D:V.45 Salt bridges: C:R.49 PDC.50: 9 residues within 4Å: Chain C: A.28, R.49 Chain D: T.30, G.31, V.45, L.46, T.47 Ligands: PDC.49, TB.55 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.45 Salt bridges: C:R.49 PDC.58: 6 residues within 4Å: Chain C: A.55, T.56 Chain D: H.77 Ligands: PDC.61, PDC.65, TB.73 2 PLIP interactions: 2 interactions with chain D Water bridges: D:N.75 Salt bridges: D:H.77 PDC.59: 4 residues within 4Å: Chain D: R.43 Ligands: PDC.63, PDC.64, TB.72 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.43 PDC.60: 8 residues within 4Å: Chain B: W.110, K.111 Chain D: G.38, N.39, R.74 Ligands: PDC.66, PDC.67, TB.75 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Salt bridges: B:K.111 Hydrophobic interactions: D:N.39 Hydrogen bonds: D:G.38 PDC.61: 10 residues within 4Å: Chain C: A.53 Chain D: K.70, N.71, N.72, Y.73, R.74, N.75 Ligands: PDC.58, PDC.65, TB.73 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.75 Salt bridges: D:H.77 PDC.62: 5 residues within 4Å: Chain D: E.34, E.41, S.42 Ligands: PDC.63, TB.71 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.34, D:S.42 PDC.63: 7 residues within 4Å: Chain D: E.41, S.42, R.43, Y.73 Ligands: PDC.59, PDC.62, TB.71 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.73 Water bridges: D:R.43, D:R.43 Salt bridges: D:R.43 PDC.64: 2 residues within 4Å: Ligands: PDC.59, TB.72 No protein-ligand interaction detected (PLIP) PDC.65: 5 residues within 4Å: Chain D: R.74, N.75 Ligands: PDC.58, PDC.61, TB.73 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.75 PDC.66: 5 residues within 4Å: Chain B: K.111 Ligands: PDC.28, PDC.60, PDC.67, TB.75 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.111, B:K.111 Salt bridges: B:K.111 PDC.67: 11 residues within 4Å: Chain B: K.111 Chain D: N.39, A.76, S.78, L.100, S.102, L.114 Ligands: PDC.60, PDC.66, BTN.70, TB.75 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Salt bridges: B:K.111 Hydrophobic interactions: D:L.114 PDC.68: 5 residues within 4Å: Chain C: V.45 Chain D: D.26, R.49 Ligands: PDC.69, TB.74 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:D.26 Water bridges: D:R.49, C:V.45 Salt bridges: D:R.49 PDC.69: 9 residues within 4Å: Chain C: T.30, G.31, V.45, L.46, T.47 Chain D: A.28, R.49 Ligands: PDC.68, TB.74 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Salt bridges: D:R.49 Hydrophobic interactions: C:V.45

4 x BTN: BIOTIN(Non-covalent)

BTN.13: 19 residues within 4Å: Chain A: N.13, L.15, S.17, Y.33, S.35, V.37, G.38, N.39, A.40, W.69, A.76, S.78, T.80, W.82, W.98, L.100, D.118 Chain C: W.110 Ligands: PDC.10 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.69, A:W.69, A:W.69, A:L.100 Hydrogen bonds: A:N.13, A:S.17, A:S.35, A:N.39, A:S.78, A:D.118 BTN.32: 19 residues within 4Å: Chain B: N.13, L.15, S.17, Y.33, S.35, V.37, G.38, N.39, A.40, W.69, A.76, S.78, T.80, W.82, W.98, L.100, D.118 Chain D: W.110 Ligands: PDC.29 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.69, B:W.69, B:W.69, B:L.100 Hydrogen bonds: B:N.13, B:S.17, B:S.35, B:N.39, B:S.78, B:D.118 BTN.51: 19 residues within 4Å: Chain A: W.110 Chain C: N.13, L.15, S.17, Y.33, S.35, V.37, G.38, N.39, A.40, W.69, A.76, S.78, T.80, W.82, W.98, L.100, D.118 Ligands: PDC.48 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.69, C:W.69, C:W.69, C:L.100 Hydrogen bonds: C:N.13, C:S.17, C:S.35, C:N.39, C:S.78, C:D.118 BTN.70: 19 residues within 4Å: Chain B: W.110 Chain D: N.13, L.15, S.17, Y.33, S.35, V.37, G.38, N.39, A.40, W.69, A.76, S.78, T.80, W.82, W.98, L.100, D.118 Ligands: PDC.67 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.69, D:W.69, D:W.69, D:L.100 Hydrogen bonds: D:N.13, D:S.17, D:S.35, D:N.39, D:S.78, D:D.118

20 x TB: TERBIUM(III) ION(Non-functional Binders)

TB.14: 2 residues within 4Å: Ligands: PDC.5, PDC.6 Ligand excluded by PLIP TB.15: 2 residues within 4Å: Ligands: PDC.2, PDC.7 Ligand excluded by PLIP TB.16: 3 residues within 4Å: Ligands: PDC.1, PDC.4, PDC.8 Ligand excluded by PLIP TB.17: 3 residues within 4Å: Chain A: R.49 Ligands: PDC.11, PDC.12 Ligand excluded by PLIP TB.18: 3 residues within 4Å: Ligands: PDC.3, PDC.9, PDC.10 Ligand excluded by PLIP TB.33: 2 residues within 4Å: Ligands: PDC.24, PDC.25 Ligand excluded by PLIP TB.34: 2 residues within 4Å: Ligands: PDC.21, PDC.26 Ligand excluded by PLIP TB.35: 3 residues within 4Å: Ligands: PDC.20, PDC.23, PDC.27 Ligand excluded by PLIP TB.36: 3 residues within 4Å: Chain B: R.49 Ligands: PDC.30, PDC.31 Ligand excluded by PLIP TB.37: 3 residues within 4Å: Ligands: PDC.22, PDC.28, PDC.29 Ligand excluded by PLIP TB.52: 2 residues within 4Å: Ligands: PDC.43, PDC.44 Ligand excluded by PLIP TB.53: 2 residues within 4Å: Ligands: PDC.40, PDC.45 Ligand excluded by PLIP TB.54: 3 residues within 4Å: Ligands: PDC.39, PDC.42, PDC.46 Ligand excluded by PLIP TB.55: 3 residues within 4Å: Chain C: R.49 Ligands: PDC.49, PDC.50 Ligand excluded by PLIP TB.56: 3 residues within 4Å: Ligands: PDC.41, PDC.47, PDC.48 Ligand excluded by PLIP TB.71: 2 residues within 4Å: Ligands: PDC.62, PDC.63 Ligand excluded by PLIP TB.72: 2 residues within 4Å: Ligands: PDC.59, PDC.64 Ligand excluded by PLIP TB.73: 3 residues within 4Å: Ligands: PDC.58, PDC.61, PDC.65 Ligand excluded by PLIP TB.74: 3 residues within 4Å: Chain D: R.49 Ligands: PDC.68, PDC.69 Ligand excluded by PLIP TB.75: 3 residues within 4Å: Ligands: PDC.60, PDC.66, PDC.67 Ligand excluded by PLIP

4 x NA: SODIUM ION(Non-functional Binders)

NA.19: 9 residues within 4Å: Chain A: T.47, G.48, W.65, T.66 Chain B: T.47, G.48, W.65, T.66 Ligands: NA.38 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.66, B:T.66, A:T.66 NA.38: 9 residues within 4Å: Chain A: T.47, G.48, W.65, T.66 Chain B: T.47, G.48, W.65, T.66 Ligands: NA.19 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.66, A:T.66, A:T.66 NA.57: 9 residues within 4Å: Chain C: T.47, G.48, W.65, T.66 Chain D: T.47, G.48, W.65, T.66 Ligands: NA.76 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.66, D:T.66, C:T.66 NA.76: 9 residues within 4Å: Chain C: T.47, G.48, W.65, T.66 Chain D: T.47, G.48, W.65, T.66 Ligands: NA.57 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.47, D:T.66, C:T.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bandara, R.A.M.S.S. et al., Co-crystallization of streptavidin-biotin complex with a lanthanide-ligand complex gives rise to a novel crystal form. To be Published

Release Date

2014-01-29

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Streptavidin

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