SMTL ID : 1b4n.1

FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE FROM PYROCOCCUS FURIOSUS, COMPLEXED WITH GLUTARATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: G.179, E.304, D.306 Ligands: PTE.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.179, A:E.304, A:D.306, H2O.2, H2O.2 CA.5: 4 residues within 4Å: Chain B: G.179, E.304, D.306 Ligands: PTE.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.179, B:E.304, B:D.306, H2O.4, H2O.4 CA.9: 5 residues within 4Å: Chain C: G.179, E.304, D.306, N.309 Ligands: PTE.12 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:G.179, C:E.304, C:D.306, H2O.6, H2O.6 CA.13: 4 residues within 4Å: Chain D: G.179, E.304, D.306 Ligands: PTE.16 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:G.179, D:E.304, D:D.306, H2O.8, H2O.8

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

SF4.2: 13 residues within 4Å: Chain A: S.72, K.75, R.180, W.235, G.283, C.284, C.287, M.289, P.290, C.291, C.491, L.493 Ligands: PTE.4 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.284, A:C.287, A:C.291, A:C.491 SF4.6: 12 residues within 4Å: Chain B: S.72, K.75, R.180, G.283, C.284, C.287, M.289, P.290, C.291, C.491, L.493 Ligands: PTE.8 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.284, B:C.287, B:C.291, B:C.491 SF4.10: 12 residues within 4Å: Chain C: S.72, K.75, R.180, W.235, G.283, C.284, C.287, M.289, P.290, C.291, C.491 Ligands: PTE.12 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.284, C:C.287, C:C.291, C:C.491 SF4.14: 11 residues within 4Å: Chain D: S.72, K.75, R.180, G.283, C.284, C.287, M.289, P.290, C.291, C.491 Ligands: PTE.16 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.284, D:C.287, D:C.291, D:C.491

4 x GUA: GLUTARIC ACID(Non-covalent)

GUA.3: 11 residues within 4Å: Chain A: Y.307, E.308, Y.416, H.437, W.441, R.481, R.492, L.493, V.496, E.497 Ligands: PTE.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.441 Hydrogen bonds: A:E.308 Salt bridges: A:H.437, A:R.481, A:R.492 GUA.7: 11 residues within 4Å: Chain B: Y.307, E.308, Y.416, H.437, W.441, R.481, R.492, L.493, V.496, E.497 Ligands: PTE.8 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.441 Hydrogen bonds: B:Y.416 Salt bridges: B:H.437, B:R.481, B:R.492 GUA.11: 11 residues within 4Å: Chain C: Y.307, E.308, Y.416, H.437, W.441, R.481, R.492, L.493, V.496, E.497 Ligands: PTE.12 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.441, C:L.493, C:V.496 Hydrogen bonds: C:Y.416 Salt bridges: C:H.437, C:R.481, C:R.492 GUA.15: 11 residues within 4Å: Chain D: Y.307, E.308, Y.416, H.437, W.441, R.481, R.492, L.493, V.496, E.497 Ligands: PTE.16 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.441, D:V.496 Salt bridges: D:H.437, D:R.481, D:R.492

4 x PTE: TUNGSTOPTERIN COFACTOR(Non-covalent)

PTE.4: 35 residues within 4Å: Chain A: K.75, G.91, N.92, L.93, G.94, G.179, R.180, A.181, A.182, G.183, R.184, T.240, C.284, D.306, E.308, N.309, A.332, D.333, M.337, D.338, T.339, I.340, H.436, H.437, K.438, F.485, E.486, T.489, A.490, C.491, R.492, L.493 Ligands: CA.1, SF4.2, GUA.3 26 PLIP interactions: 24 interactions with chain A, 2 Ligand-Water interactions, Hydrogen bonds: A:K.75, A:N.92, A:G.94, A:G.94, A:G.179, A:A.181, A:G.183, A:R.184, A:N.309, A:M.337, A:T.339, A:A.490, A:R.492, A:R.492 Water bridges: A:E.304, A:R.492, A:R.492 Salt bridges: A:K.75, A:R.180, A:D.333, A:H.436, A:K.438, A:E.486 Metal complexes: A:N.92, H2O.2, H2O.2 PTE.8: 34 residues within 4Å: Chain B: K.75, G.91, N.92, L.93, G.94, G.179, R.180, A.181, A.182, G.183, R.184, C.284, D.306, E.308, N.309, A.332, D.333, M.337, D.338, T.339, I.340, H.436, H.437, K.438, F.485, E.486, T.489, A.490, C.491, R.492, L.493 Ligands: CA.5, SF4.6, GUA.7 28 PLIP interactions: 27 interactions with chain B, 1 Ligand-Water interactions, Hydrogen bonds: B:K.75, B:N.92, B:G.94, B:G.94, B:G.179, B:A.181, B:G.183, B:R.184, B:N.309, B:M.337, B:D.338, B:T.339, B:K.438, B:A.490, B:R.492, B:R.492 Water bridges: B:E.304, B:R.492, B:R.492 Salt bridges: B:K.75, B:R.180, B:D.333, B:H.436, B:K.438, B:E.486 Metal complexes: B:N.92, B:A.181, H2O.4 PTE.12: 34 residues within 4Å: Chain C: K.75, G.91, N.92, L.93, G.94, G.179, R.180, A.181, A.182, G.183, R.184, C.284, D.306, E.308, N.309, A.332, D.333, M.337, D.338, T.339, I.340, H.436, H.437, K.438, F.485, E.486, T.489, A.490, C.491, R.492, L.493 Ligands: CA.9, SF4.10, GUA.11 29 PLIP interactions: 27 interactions with chain C, 2 Ligand-Water interactions, Hydrogen bonds: C:K.75, C:N.92, C:G.94, C:G.94, C:G.179, C:A.181, C:G.183, C:R.184, C:D.306, C:N.309, C:M.337, C:D.338, C:T.339, C:K.438, C:T.489, C:A.490, C:R.492, C:R.492 Water bridges: C:R.180, C:R.492 Salt bridges: C:K.75, C:R.180, C:D.333, C:H.436, C:K.438, C:E.486 Metal complexes: C:N.92, H2O.5, H2O.6 PTE.16: 34 residues within 4Å: Chain D: K.75, G.91, N.92, L.93, G.94, G.179, R.180, A.181, A.182, G.183, R.184, C.284, D.306, E.308, N.309, A.332, D.333, M.337, D.338, T.339, I.340, H.436, H.437, K.438, F.485, E.486, T.489, A.490, C.491, R.492, L.493 Ligands: CA.13, SF4.14, GUA.15 27 PLIP interactions: 26 interactions with chain D, 1 Ligand-Water interactions, Hydrogen bonds: D:K.75, D:N.92, D:G.94, D:G.94, D:G.179, D:A.181, D:G.183, D:R.184, D:D.306, D:N.309, D:M.337, D:D.338, D:T.339, D:K.438, D:T.489, D:A.490, D:R.492, D:R.492 Salt bridges: D:K.75, D:R.180, D:D.333, D:H.436, D:K.438, D:E.486 Metal complexes: D:N.92, D:A.181, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, Y. et al., Formaldehyde ferredoxin oxidoreductase from Pyrococcus furiosus: the 1.85 A resolution crystal structure and its mechanistic implications. J.Mol.Biol. (1999)

Release Date

1999-05-18

Peptides

FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE

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