SMTL ID : 3zzx.1

Crystallographic structure of thioredoxin from Litopenaeus vannamei

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-tetramer

Ligands

2 x DTU: (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Non-covalent)

DTU.1: 1 residues within 4Å: Chain A: S.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.48 DTU.14: 1 residues within 4Å: Chain C: S.48 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.48

14 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 2 residues within 4Å: Chain A: L.89, S.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.90, A:S.90 ACT.3: 5 residues within 4Å: Chain A: K.6, D.7, E.61, C.62, D.64 No protein-ligand interaction detected (PLIP) ACT.4: 4 residues within 4Å: Chain A: D.26, Y.28, A.39, K.56 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.39, A:K.56 Hydrogen bonds: A:C.35 Salt bridges: A:K.56 ACT.5: 2 residues within 4Å: Chain A: F.11, N.69 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.11 Hydrogen bonds: A:N.69 ACT.6: 1 residues within 4Å: Chain A: K.41 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.41 Salt bridges: A:K.41 ACT.12: 3 residues within 4Å: Chain B: N.69, K.85, S.88 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.85 ACT.13: 2 residues within 4Å: Chain B: D.51, K.105 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.105 Salt bridges: B:K.105 ACT.15: 2 residues within 4Å: Chain C: L.89, S.90 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.90, C:S.90 ACT.16: 5 residues within 4Å: Chain C: K.6, D.7, E.61, C.62, D.64 No protein-ligand interaction detected (PLIP) ACT.17: 4 residues within 4Å: Chain C: D.26, Y.28, A.39, K.56 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.39, C:K.56 Hydrogen bonds: C:C.35 Salt bridges: C:K.56 ACT.18: 2 residues within 4Å: Chain C: F.11, N.69 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.11 Hydrogen bonds: C:N.69 ACT.19: 1 residues within 4Å: Chain C: K.41 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.41 Salt bridges: C:K.41 ACT.25: 3 residues within 4Å: Chain D: N.69, K.85, S.88 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.85 ACT.26: 2 residues within 4Å: Chain D: D.51, K.105 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.105 Salt bridges: D:K.105

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: T.12, L.15, N.16, N.82, G.83 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.19, A:G.19 GOL.8: 4 residues within 4Å: Chain A: A.92, N.93, Y.94, D.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.94, A:D.95, A:D.95, A:D.95 GOL.9: 2 residues within 4Å: Chain A: K.41, Y.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.41, A:Y.94 GOL.10: 4 residues within 4Å: Chain A: E.17, A.18, K.21, V.53 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.17, A:E.17 Water bridges: A:A.18, A:K.21 GOL.20: 5 residues within 4Å: Chain C: T.12, L.15, N.16, N.82, G.83 2 PLIP interactions: 2 interactions with chain C Water bridges: C:G.19, C:G.19 GOL.21: 4 residues within 4Å: Chain C: A.92, N.93, Y.94, D.95 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.94, C:D.95, C:D.95 GOL.22: 2 residues within 4Å: Chain C: K.41, Y.94 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.41, C:Y.94 Water bridges: C:E.44 GOL.23: 4 residues within 4Å: Chain C: E.17, A.18, K.21, V.53 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.17 Water bridges: C:A.18, C:K.21

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

SO4.11: 6 residues within 4Å: Chain B: K.13, E.17 Chain D: A.18, G.19, N.20, K.21 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:A.18, D:N.20, D:K.21 Salt bridges: D:K.21, B:K.13 Water bridges: B:K.13, B:Q.14 SO4.24: 6 residues within 4Å: Chain B: A.18, G.19, N.20, K.21 Chain D: K.13, E.17 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B Water bridges: D:K.13, D:Q.14 Salt bridges: D:K.13, B:K.21 Hydrogen bonds: B:A.18, B:N.20, B:K.21

Links

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Citation

Campos-Acevedo, A.A. et al., Expression, Purification, Crystallization and X-Ray Crystallographic Studies of Different Redox States of the Active Site of Thioredoxin 1 from the Whiteleg Shrimp Litopenaeus Vannamei. Acta Crystallogr.,Sect.F (2013)

Release Date

2012-09-26

Peptides

THIOREDOXIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

THIOREDOXIN

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