SMTL ID : 3jtm.2 (1 other biounit)

Structure of recombinant formate dehydrogenase from Arabidopsis thaliana

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.327, P.335 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.336, A:T.336, A:T.336 Salt bridges: A:R.327 SO4.2: 3 residues within 4Å: Chain A: Y.157, R.158 Chain B: K.18 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.157 Water bridges: A:R.158, A:N.299 Salt bridges: A:R.158, B:K.18 SO4.17: 2 residues within 4Å: Chain B: R.327, P.335 4 PLIP interactions: 4 interactions with chain B Water bridges: B:T.336, B:T.336, B:T.336 Salt bridges: B:R.327 SO4.18: 3 residues within 4Å: Chain A: K.18 Chain B: Y.157, R.158 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:R.158, B:N.299 Salt bridges: B:R.158, A:K.18

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: K.177, L.196, Q.197, M.198, A.199, L.202 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: V.26, E.27, N.28, A.29, R.33, V.45 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: P.70, F.71, G.94, I.95, N.119, G.308, Y.317 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: L.23, L.30, G.31, I.32, K.322 Ligands: GOL.15 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: N.119, V.123, I.175, N.255, A.256 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: R.263, P.285, P.289, D.291, H.292 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: M.135, Y.160, K.165, D.222 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain A: I.81, K.82, A.84, K.85 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: I.95, G.96, S.97, D.98, E.114, I.340 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain A: G.173, R.174 Ligands: GOL.16 Ligand excluded by PLIP GOL.15: 2 residues within 4Å: Chain A: K.322 Ligands: GOL.6 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain A: A.172, G.173, D.194, L.196 Ligands: GOL.13 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain B: K.177, L.196, Q.197, M.198, A.199, L.202 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain B: V.26, E.27, N.28, A.29, R.33, V.45 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain B: P.70, F.71, G.94, I.95, N.119, G.308, Y.317 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: L.23, L.30, G.31, I.32, K.322 Ligands: GOL.31 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain B: N.119, V.123, I.175, N.255, A.256 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain B: R.263, P.285, P.289, D.291, H.292 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain B: M.135, Y.160, K.165, D.222 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain B: I.81, K.82, A.84, K.85 Ligand excluded by PLIP GOL.28: 6 residues within 4Å: Chain B: I.95, G.96, S.97, D.98, E.114, I.340 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain B: G.173, R.174 Ligands: GOL.32 Ligand excluded by PLIP GOL.31: 2 residues within 4Å: Chain B: K.322 Ligands: GOL.22 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain B: A.172, G.173, D.194, L.196 Ligands: GOL.29 Ligand excluded by PLIP

4 x AZI: AZIDE ION(Non-covalent)

AZI.8: 2 residues within 4Å: Chain A: E.332, D.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.333, A:D.333 AZI.14: 5 residues within 4Å: Chain A: L.134, N.137, G.276, G.277, N.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.134, A:N.299 Water bridges: A:N.137 AZI.24: 2 residues within 4Å: Chain B: E.332, D.333 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.333, B:D.333 AZI.30: 5 residues within 4Å: Chain B: L.134, N.137, G.276, G.277, N.299 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.276 Water bridges: B:L.134, B:M.135, B:N.137, B:R.158, B:G.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timofeev, V.I. et al., Structure of recombinant formate dehydrogenase from Arabidopsis thaliana. to be published

Release Date

2010-09-15

Peptides

Formate dehydrogenase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Formate dehydrogenase, mitochondrial

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