SMTL ID : 4tpu.1

CRYSTAL STRUCTURE OF FERREDOXIN-DEPENDENT DISULFIDE REDUCTASE FROM METHANOSARCINA ACETIVORANS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.173 SO4.17: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.173 SO4.33: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.173

3 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 13 residues within 4Å: Chain A: C.50, P.51, R.53, I.65, C.67, P.68, C.69, R.72, C.82, Y.83, C.84, L.86, Y.87 5 PLIP interactions: 5 interactions with chain A, Metal complexes: A:C.50, A:C.67, A:C.69, A:C.82, A:C.84 SF4.18: 13 residues within 4Å: Chain B: C.50, P.51, R.53, I.65, C.67, P.68, C.69, R.72, C.82, Y.83, C.84, L.86, Y.87 5 PLIP interactions: 5 interactions with chain B, Metal complexes: B:C.50, B:C.67, B:C.69, B:C.82, B:C.84 SF4.34: 13 residues within 4Å: Chain C: C.50, P.51, R.53, I.65, C.67, P.68, C.69, R.72, C.82, Y.83, C.84, L.86, Y.87 5 PLIP interactions: 5 interactions with chain C, Metal complexes: C:C.50, C:C.67, C:C.69, C:C.82, C:C.84

3 x FE: FE (III) ION(Non-covalent)

FE.3: 7 residues within 4Å: Chain A: C.142, V.144, C.145, Y.147, C.158, I.160, C.161 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.142, A:C.145, A:C.158, A:C.161 FE.19: 7 residues within 4Å: Chain B: C.142, V.144, C.145, Y.147, C.158, I.160, C.161 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.142, B:C.145, B:C.158, B:C.161 FE.35: 7 residues within 4Å: Chain C: C.142, V.144, C.145, Y.147, C.158, I.160, C.161 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.142, C:C.145, C:C.158, C:C.161

6 x URE: UREA(Non-functional Binders)

URE.4: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.141 URE.5: 4 residues within 4Å: Chain A: C.52, Y.83, C.84 Ligands: BR.13 No protein-ligand interaction detected (PLIP) URE.20: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.141 URE.21: 4 residues within 4Å: Chain B: C.52, Y.83, C.84 Ligands: BR.29 No protein-ligand interaction detected (PLIP) URE.36: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.141 URE.37: 4 residues within 4Å: Chain C: C.52, Y.83, C.84 Ligands: BR.45 No protein-ligand interaction detected (PLIP)

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

NA.6: 3 residues within 4Å: Chain A: P.108, R.109, R.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.109 NA.8: 5 residues within 4Å: Chain A: L.76, N.77, S.89 Chain C: G.156 Ligands: BR.7 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:G.156, A:L.76 Water bridges: C:K.165, A:N.77 NA.9: 5 residues within 4Å: Chain A: P.74 Chain C: K.137, M.151, D.152 Ligands: BR.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.152 Water bridges: C:D.152 NA.15: 3 residues within 4Å: Chain A: K.59, I.66 Ligands: BR.11 No protein-ligand interaction detected (PLIP) NA.22: 3 residues within 4Å: Chain B: P.108, R.109, R.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.109 NA.24: 5 residues within 4Å: Chain A: G.156 Chain B: L.76, N.77, S.89 Ligands: BR.23 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.156, B:L.76 Water bridges: A:K.165, B:N.77 NA.25: 5 residues within 4Å: Chain A: K.137, M.151, D.152 Chain B: P.74 Ligands: BR.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.152, A:D.152 NA.31: 3 residues within 4Å: Chain B: K.59, I.66 Ligands: BR.27 No protein-ligand interaction detected (PLIP) NA.38: 3 residues within 4Å: Chain C: P.108, R.109, R.112 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.109 NA.40: 5 residues within 4Å: Chain B: G.156 Chain C: L.76, N.77, S.89 Ligands: BR.39 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:L.76, B:G.156 Water bridges: C:N.77, B:K.165 NA.41: 5 residues within 4Å: Chain B: K.137, M.151, D.152 Chain C: P.74 Ligands: BR.42 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.152, B:D.152 NA.47: 3 residues within 4Å: Chain C: K.59, I.66 Ligands: BR.43 No protein-ligand interaction detected (PLIP)

21 x BR: BROMIDE ION(Non-covalent)(Non-functional Binders)

BR.7: 7 residues within 4Å: Chain A: Y.22, H.23, L.76, S.89, D.90 Chain C: G.156 Ligands: NA.8 Ligand excluded by PLIP BR.10: 6 residues within 4Å: Chain A: P.74, N.77 Chain C: M.151, D.152, E.153 Ligands: NA.9 Ligand excluded by PLIP BR.11: 5 residues within 4Å: Chain A: Y.47, W.48, K.59, I.66 Ligands: NA.15 Ligand excluded by PLIP BR.12: 3 residues within 4Å: Chain A: W.140, E.169, R.170 Ligand excluded by PLIP BR.13: 3 residues within 4Å: Chain A: Y.83, I.102 Ligands: URE.5 Ligand excluded by PLIP BR.14: 3 residues within 4Å: Chain C: R.164, K.165, E.166 Ligand excluded by PLIP BR.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP BR.23: 7 residues within 4Å: Chain A: G.156 Chain B: Y.22, H.23, L.76, S.89, D.90 Ligands: NA.24 Ligand excluded by PLIP BR.26: 6 residues within 4Å: Chain A: M.151, D.152, E.153 Chain B: P.74, N.77 Ligands: NA.25 Ligand excluded by PLIP BR.27: 5 residues within 4Å: Chain B: Y.47, W.48, K.59, I.66 Ligands: NA.31 Ligand excluded by PLIP BR.28: 3 residues within 4Å: Chain B: W.140, E.169, R.170 Ligand excluded by PLIP BR.29: 3 residues within 4Å: Chain B: Y.83, I.102 Ligands: URE.21 Ligand excluded by PLIP BR.30: 3 residues within 4Å: Chain A: R.164, K.165, E.166 Ligand excluded by PLIP BR.32: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP BR.39: 7 residues within 4Å: Chain B: G.156 Chain C: Y.22, H.23, L.76, S.89, D.90 Ligands: NA.40 Ligand excluded by PLIP BR.42: 6 residues within 4Å: Chain B: M.151, D.152, E.153 Chain C: P.74, N.77 Ligands: NA.41 Ligand excluded by PLIP BR.43: 5 residues within 4Å: Chain C: Y.47, W.48, K.59, I.66 Ligands: NA.47 Ligand excluded by PLIP BR.44: 3 residues within 4Å: Chain C: W.140, E.169, R.170 Ligand excluded by PLIP BR.45: 3 residues within 4Å: Chain C: Y.83, I.102 Ligands: URE.37 Ligand excluded by PLIP BR.46: 3 residues within 4Å: Chain B: R.164, K.165, E.166 Ligand excluded by PLIP BR.48: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A.K. et al., Structural and Biochemical Characterization of a Ferredoxin:Thioredoxin Reductase-like Enzyme from Methanosarcina acetivorans. Biochemistry (2015)

Release Date

2015-05-13

Peptides

Rubredoxin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Rubredoxin