SMTL ID : 2y3f.1

Traptavidin, biotin bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-tetramer

Ligands

4 x BTN: BIOTIN(Non-covalent)

BTN.1: 19 residues within 4Å: Chain A: N.12, L.14, S.16, Y.32, S.34, V.36, G.37, N.38, A.39, W.68, A.75, S.77, T.79, W.81, W.97, L.99, D.117 Chain B: W.109 Ligands: GOL.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.39, A:W.68, A:W.68, A:W.68, A:L.99 Hydrogen bonds: A:N.12, A:S.16, A:Y.32, A:S.34, A:N.38, A:S.77, A:S.77, A:D.117 BTN.5: 19 residues within 4Å: Chain A: W.109 Chain B: N.12, L.14, S.16, Y.32, S.34, V.36, G.37, N.38, A.39, W.68, A.75, S.77, T.79, W.81, W.97, L.99, D.117 Ligands: GOL.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.39, B:W.68, B:W.68, B:W.68, B:L.99 Hydrogen bonds: B:N.12, B:S.16, B:Y.32, B:S.34, B:N.38, B:S.77, B:S.77, B:D.117 BTN.9: 19 residues within 4Å: Chain C: N.12, L.14, S.16, Y.32, S.34, V.36, G.37, N.38, A.39, W.68, A.75, S.77, T.79, W.81, W.97, L.99, D.117 Chain D: W.109 Ligands: GOL.10 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:A.39, C:W.68, C:W.68, C:W.68, C:L.99 Hydrogen bonds: C:N.12, C:S.16, C:S.34, C:N.38, C:S.77, C:S.77, C:D.117 BTN.13: 19 residues within 4Å: Chain C: W.109 Chain D: N.12, L.14, S.16, Y.32, S.34, V.36, G.37, N.38, A.39, W.68, A.75, S.77, T.79, W.81, W.97, L.99, D.117 Ligands: GOL.14 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:A.39, D:W.68, D:W.68, D:W.68, D:L.99 Hydrogen bonds: D:N.12, D:S.16, D:S.34, D:N.38, D:S.77, D:S.77, D:D.117

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: S.101 Chain B: W.109 Ligands: BTN.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.101 GOL.3: 10 residues within 4Å: Chain A: S.82, G.83, Q.84, N.94, T.95, Q.96 Chain D: T.100, A.108, S.111, T.112 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:T.100, D:S.111, D:T.112, A:S.82, A:Q.84, A:Q.96, A:Q.96 Water bridges: D:A.108, D:S.111, A:T.95 GOL.4: 1 residues within 4Å: Chain A: D.56 No protein-ligand interaction detected (PLIP) GOL.6: 3 residues within 4Å: Chain A: W.109 Chain B: S.101 Ligands: BTN.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.101 GOL.7: 10 residues within 4Å: Chain B: S.82, G.83, Q.84, N.94, T.95, Q.96 Chain C: T.100, A.108, S.111, T.112 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:S.82, B:Q.84, B:Q.96, B:Q.96, C:T.100, C:S.111, C:T.112 Water bridges: B:T.95, C:A.108, C:S.111 GOL.8: 1 residues within 4Å: Chain B: D.56 No protein-ligand interaction detected (PLIP) GOL.10: 3 residues within 4Å: Chain C: S.101 Chain D: W.109 Ligands: BTN.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.101 GOL.11: 10 residues within 4Å: Chain B: T.100, A.108, S.111, T.112 Chain C: S.82, G.83, Q.84, N.94, T.95, Q.96 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:S.82, C:Q.84, C:Q.96, C:Q.96, B:S.111 Water bridges: C:T.95, B:A.108, B:S.111 GOL.12: 1 residues within 4Å: Chain C: D.56 No protein-ligand interaction detected (PLIP) GOL.14: 3 residues within 4Å: Chain C: W.109 Chain D: S.101 Ligands: BTN.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.101 GOL.15: 10 residues within 4Å: Chain A: T.100, A.108, S.111, T.112 Chain D: S.82, G.83, Q.84, N.94, T.95, Q.96 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:S.82, D:Q.84, D:Q.96, D:Q.96, A:S.111 Water bridges: D:T.95, A:A.108, A:S.111 GOL.16: 1 residues within 4Å: Chain D: D.56 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chivers, C.E. et al., How the Biotin-Streptavidin Interaction Was Made Even Stronger: Investigation Via Crystallography and a Chimeric Tetramer. Biochem.J. (2011)

Release Date

2011-02-16

Peptides

STREPTAVIDIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

STREPTAVIDIN

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