SMTL ID : 4jlw.1

Crystal structure of formaldehyde dehydrogenase from Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: C.98, G.99, C.101, C.104, C.112, L.113, T.114 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.98, A:C.101, A:C.104, A:C.112 ZN.2: 5 residues within 4Å: Chain A: C.47, S.49, H.68, D.170 Ligands: NAD.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.47, A:H.68, A:D.170 ZN.5: 7 residues within 4Å: Chain B: C.98, G.99, C.101, C.104, C.112, L.113, T.114 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.98, B:C.101, B:C.104, B:C.112 ZN.6: 5 residues within 4Å: Chain B: C.47, S.49, H.68, D.170 Ligands: NAD.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.47, B:H.68, B:D.170 ZN.10: 6 residues within 4Å: Chain C: C.98, G.99, C.101, C.104, C.112, L.113 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.98, C:C.101, C:C.104, C:C.112 ZN.11: 4 residues within 4Å: Chain C: C.47, H.68, D.170 Ligands: NAD.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.47, C:H.68, C:D.170 ZN.15: 7 residues within 4Å: Chain D: C.98, G.99, C.101, C.104, C.112, L.113, T.114 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.98, D:C.101, D:C.104, D:C.112 ZN.16: 5 residues within 4Å: Chain D: C.47, S.49, H.68, D.170 Ligands: NAD.17 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.47, D:H.68, D:D.170, H2O.14

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

NAD.3: 31 residues within 4Å: Chain A: C.47, G.48, S.49, Q.51, H.52, F.94, D.170, T.174, G.194, G.196, P.197, V.198, G.217, D.218, V.219, R.223, A.262, V.263, A.267, R.268, H.270, V.283, P.300, G.301, L.302, G.337, Q.338, T.339, F.380 Chain B: W.328 Ligands: ZN.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:T.174, A:V.198 Hydrogen bonds: A:G.48, A:G.48, A:T.174, A:V.198, A:R.223, A:R.223, A:V.263, A:R.268, A:H.270, A:L.302, A:G.337, A:Q.338, A:T.339, A:T.339 Water bridges: A:Q.51, A:Q.51 Salt bridges: A:R.223 NAD.7: 31 residues within 4Å: Chain A: W.328 Chain B: C.47, G.48, S.49, H.52, F.94, D.170, T.174, G.194, G.196, P.197, V.198, G.217, D.218, V.219, N.220, R.223, A.262, V.263, A.267, R.268, H.270, V.283, P.300, G.301, L.302, G.337, Q.338, T.339, F.380 Ligands: ZN.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:T.174 Hydrogen bonds: B:G.48, B:Q.51, B:H.52, B:T.174, B:V.198, B:R.223, B:R.223, B:V.263, B:R.268, B:R.268, B:L.302, B:G.337, B:Q.338, B:T.339, B:T.339 Salt bridges: B:R.223 NAD.12: 31 residues within 4Å: Chain C: C.47, G.48, S.49, H.52, F.94, D.170, T.174, G.194, G.196, P.197, V.198, G.199, G.217, D.218, V.219, R.223, A.262, V.263, A.267, R.268, H.270, V.283, P.300, G.301, L.302, G.337, Q.338, T.339, F.380 Chain D: W.328 Ligands: ZN.11 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:T.174 Hydrogen bonds: C:G.48, C:Q.51, C:H.52, C:G.196, C:V.198, C:G.199, C:R.223, C:V.263, C:R.268, C:H.270, C:P.300, C:L.302, C:Q.338, C:T.339 Water bridges: C:R.223 Salt bridges: C:R.223 NAD.17: 34 residues within 4Å: Chain C: W.328 Chain D: C.47, G.48, S.49, Q.51, H.52, F.94, D.170, T.174, G.194, G.196, P.197, V.198, G.199, G.217, D.218, V.219, N.220, R.223, L.237, A.262, V.263, A.267, R.268, H.270, V.283, P.300, G.301, L.302, G.337, Q.338, T.339, F.380 Ligands: ZN.16 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:T.174 Hydrogen bonds: D:G.48, D:Q.51, D:H.52, D:V.198, D:G.199, D:V.219, D:R.223, D:V.263, D:R.268, D:H.270, D:P.300, D:L.302, D:Q.338, D:T.339 Water bridges: D:G.196 Salt bridges: D:R.223

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

SO4.4: 5 residues within 4Å: Chain A: P.242, L.243, H.244, H.270, S.286 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.243, A:H.244, A:H.244, A:S.286, A:S.286 Salt bridges: A:H.270 SO4.8: 5 residues within 4Å: Chain B: P.242, L.243, H.244, H.270, S.286 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.243, B:H.244 Water bridges: B:H.244 Salt bridges: B:H.244, B:H.270 SO4.9: 4 residues within 4Å: Chain B: K.239, D.240, T.241, H.272 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.240, B:T.241, B:T.241 Salt bridges: B:H.272 SO4.13: 5 residues within 4Å: Chain C: P.242, L.243, H.244, H.270, S.286 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.243, C:H.244 Salt bridges: C:H.270 SO4.14: 3 residues within 4Å: Chain C: K.239, D.240, H.272 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.240 Salt bridges: C:K.239, C:H.272 SO4.18: 5 residues within 4Å: Chain D: P.242, L.243, H.244, H.270, S.286 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.243, D:H.244, D:H.244, D:S.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liao, Y.P. et al., Structure of formaldehyde dehydrogenase from Pseudomonas aeruginosa: the binary complex with the cofactor NAD+. Acta Crystallogr.,Sect.F (2013)

Release Date

2013-10-30

Peptides

Glutathione-independent formaldehyde dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glutathione-independent formaldehyde dehydrogenase