SMTL ID : 1kol.1

Crystal structure of formaldehyde dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.46, S.48, H.67, D.169 Ligands: NAD.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.46, A:H.67, A:D.169, H2O.1 ZN.2: 6 residues within 4Å: Chain A: C.97, G.98, C.100, C.103, C.111, L.112 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.97, A:C.100, A:C.103, A:C.111 ZN.5: 5 residues within 4Å: Chain B: C.46, S.48, H.67, D.169 Ligands: NAD.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.46, B:H.67, B:D.169, H2O.19 ZN.6: 6 residues within 4Å: Chain B: C.97, G.98, C.100, C.103, C.111, L.112 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.97, B:C.100, B:C.103, B:C.111 ZN.9: 5 residues within 4Å: Chain C: C.46, S.48, H.67, D.169 Ligands: NAD.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.46, C:H.67, C:D.169, H2O.38 ZN.10: 6 residues within 4Å: Chain C: C.97, G.98, C.100, C.103, C.111, L.112 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.97, C:C.100, C:C.103, C:C.111 ZN.13: 5 residues within 4Å: Chain D: C.46, S.48, H.67, D.169 Ligands: NAD.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.46, D:H.67, D:D.169, H2O.56 ZN.14: 6 residues within 4Å: Chain D: C.97, G.98, C.100, C.103, C.111, L.112 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.97, D:C.100, D:C.103, D:C.111

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

SO4.3: 3 residues within 4Å: Chain A: P.241, L.242, H.269 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:L.242 Water bridges: A:L.238, A:D.239, A:T.240, A:H.243, A:H.269, A:G.270 Salt bridges: A:H.269 SO4.7: 3 residues within 4Å: Chain B: P.241, L.242, H.269 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:L.242 Water bridges: B:H.243, B:H.269, B:G.270, B:Q.288, B:Q.288 Salt bridges: B:H.269 SO4.11: 3 residues within 4Å: Chain C: P.241, L.242, H.269 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:L.242 Water bridges: C:L.238, C:D.239, C:T.240, C:H.269, C:G.270 Salt bridges: C:H.269 SO4.15: 3 residues within 4Å: Chain D: P.241, L.242, H.269 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:L.242 Water bridges: D:H.243, D:G.270, D:Q.288, D:Q.288 Salt bridges: D:H.269

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.4: 32 residues within 4Å: Chain A: C.46, G.47, S.48, Q.50, H.51, F.93, D.169, T.173, G.193, G.195, P.196, V.197, G.216, D.217, L.218, R.222, L.236, A.261, V.262, A.266, R.267, H.269, V.282, P.299, G.300, L.301, G.336, Q.337, T.338, F.379 Chain C: W.327 Ligands: ZN.1 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:T.173, A:V.197 Hydrogen bonds: A:G.47, A:H.51, A:G.195, A:G.195, A:V.197, A:R.222, A:R.222, A:V.262, A:R.267, A:H.269, A:P.299, A:L.301, A:T.338 Water bridges: A:Q.50, A:Q.50, A:Q.50, A:Q.50, A:Q.50, A:Q.50, A:G.198, A:N.219, A:R.267 Salt bridges: A:R.222 NAD.8: 33 residues within 4Å: Chain B: C.46, G.47, S.48, Q.50, H.51, F.93, D.169, T.173, G.193, G.195, P.196, V.197, G.216, D.217, L.218, R.222, L.236, A.261, V.262, A.266, R.267, H.269, T.281, V.282, P.299, G.300, L.301, G.336, Q.337, T.338, F.379 Chain D: W.327 Ligands: ZN.5 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:T.173, B:V.197 Hydrogen bonds: B:G.47, B:Q.50, B:H.51, B:G.195, B:G.195, B:V.197, B:R.222, B:R.222, B:V.262, B:R.267, B:H.269, B:P.299, B:L.301, B:T.338 Water bridges: B:Q.50, B:G.198, B:R.222, B:Q.337 Salt bridges: B:R.222 NAD.12: 32 residues within 4Å: Chain A: W.327 Chain C: C.46, G.47, S.48, Q.50, H.51, F.93, D.169, T.173, G.193, G.195, P.196, V.197, G.216, D.217, L.218, R.222, L.236, A.261, V.262, A.266, R.267, H.269, V.282, P.299, G.300, L.301, G.336, Q.337, T.338, F.379 Ligands: ZN.9 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:T.173, C:V.197 Hydrogen bonds: C:G.47, C:Q.50, C:H.51, C:G.195, C:G.195, C:V.197, C:R.222, C:R.222, C:V.262, C:R.267, C:H.269, C:P.299, C:L.301, C:T.338, C:T.338 Water bridges: C:Q.50, C:G.198, C:N.219, C:R.222, C:R.267, C:Q.337 Salt bridges: C:R.222 NAD.16: 33 residues within 4Å: Chain B: W.327 Chain D: C.46, G.47, S.48, Q.50, H.51, F.93, D.169, T.173, G.193, G.195, P.196, V.197, G.216, D.217, L.218, R.222, L.236, A.261, V.262, A.266, R.267, H.269, T.281, V.282, P.299, G.300, L.301, G.336, Q.337, T.338, F.379 Ligands: ZN.13 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:T.173, D:V.197 Hydrogen bonds: D:G.47, D:Q.50, D:H.51, D:G.195, D:G.195, D:V.197, D:R.222, D:R.222, D:V.262, D:R.267, D:H.269, D:P.299, D:L.301, D:T.338, D:T.338 Water bridges: D:Q.50, D:G.198, D:R.222, D:Q.337 Salt bridges: D:R.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, N. et al., Crystal Structure of Formaldehyde Dehydrogenase from Pseudomonas putida: the Structural Origin of the Tightly Bound Cofactor in Nicotinoprotein Dehydrogenases. J.mol.biol. (2002)

Release Date

2002-12-11

Peptides

formaldehyde dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

formaldehyde dehydrogenase