SMTL ID : 3mmc.1

Structure of the dissimilatory sulfite reductase from Archaeoglobus fulgidus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

hetero-2-2-mer

Ligands

4 x SRM: SIROHEME(Non-covalent)

SRM.1: 30 residues within 4Å: Chain A: R.81, R.99, G.132, S.133, T.134, G.135, D.136, I.138, Y.211, K.212, K.214, K.216, R.230, K.315, A.316, F.318, R.359, R.361 Chain B: R.60, T.134, Q.135, H.139, H.141, T.142, N.180, C.182, G.183, T.249 Ligands: GOL.4, SF4.5 40 PLIP interactions: 10 interactions with chain B, 30 interactions with chain A, Hydrophobic interactions: B:T.134, B:N.180, A:I.138, A:A.316 Hydrogen bonds: B:Q.135, B:T.142, B:T.142, B:N.180, A:G.132, A:S.133, A:T.134, A:G.135, A:D.136, A:Y.211, A:Y.211, A:A.316, A:F.318 Salt bridges: B:R.60, B:H.139, B:H.141, A:R.81, A:R.99, A:K.212, A:K.212, A:K.212, A:K.214, A:K.214, A:K.216, A:R.230, A:K.315, A:R.359, A:R.361, A:R.361 Metal complexes: B:C.182 Water bridges: A:T.97, A:R.99, A:T.134, A:R.361 pi-Cation interactions: A:K.212, A:K.214 SRM.7: 32 residues within 4Å: Chain A: C.176, M.177, C.182, E.183, F.184, N.222, D.223, C.224, N.294 Chain B: H.33, I.41, R.43, R.55, R.83, T.85, S.86, R.87, N.89, G.117, T.118, W.119, A.121, Y.126, S.129, M.170, R.172, K.271, L.272, S.273, R.276, R.319 Ligands: SF4.2 36 PLIP interactions: 7 interactions with chain A, 29 interactions with chain B, Hydrophobic interactions: A:F.184, A:N.222, A:N.294, B:R.87, B:W.119, B:L.272 Hydrogen bonds: A:M.177, B:T.85, B:S.86, B:W.119, B:S.129, B:L.272, B:S.273, B:S.273, B:S.273 Water bridges: A:R.230, A:R.230, B:S.86, B:A.121, B:A.121, B:R.276 Metal complexes: A:C.224 Salt bridges: B:H.33, B:R.43, B:R.55, B:R.55, B:R.83, B:R.87, B:R.172, B:R.172, B:K.271, B:R.276, B:R.319, B:R.319 pi-Stacking: B:W.119 pi-Cation interactions: B:R.172 SRM.8: 28 residues within 4Å: Chain C: I.79, R.81, T.97, R.99, G.132, S.133, T.134, G.135, I.138, Y.211, K.212, K.214, K.216, R.230, K.315, A.316, P.317, F.318, R.359, R.361 Chain D: Q.135, C.140, H.141, N.180, M.181, C.182, G.183 Ligands: SF4.11 29 PLIP interactions: 24 interactions with chain C, 5 interactions with chain D, Hydrophobic interactions: C:K.214, C:A.316, D:Q.135, D:N.180 Hydrogen bonds: C:T.134, C:T.134, C:G.135, C:D.136, C:Y.211, C:A.316, C:F.318, D:Q.135 Salt bridges: C:R.99, C:K.212, C:K.212, C:K.214, C:K.214, C:K.216, C:R.230, C:K.315, C:R.359, C:R.361, C:R.361, D:H.139, D:H.141 pi-Cation interactions: C:R.99, C:R.99, C:K.212, C:K.214 SRM.13: 31 residues within 4Å: Chain C: C.176, M.177, C.182, E.183, F.184, N.222, C.224, A.226, N.294 Chain D: H.33, I.41, R.43, V.53, R.55, R.83, T.85, S.86, R.87, N.89, E.91, G.117, W.119, A.121, S.129, M.170, R.172, K.271, L.272, S.273, R.276, R.319 27 PLIP interactions: 24 interactions with chain D, 3 interactions with chain C, Hydrophobic interactions: D:I.41, D:R.87, D:W.119, C:N.222 Hydrogen bonds: D:T.85, D:S.86, D:E.91, D:S.129, D:L.272, D:S.273, D:S.273, D:S.273, D:S.273, C:M.177 Salt bridges: D:H.33, D:R.43, D:R.43, D:R.55, D:R.55, D:R.83, D:R.87, D:R.172, D:K.271, D:R.276, D:R.319, D:R.319 Metal complexes: C:C.224

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

SF4.2: 11 residues within 4Å: Chain A: C.176, M.177, C.182, F.184, A.185, G.219, C.220, N.222, D.223, C.224 Ligands: SRM.7 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.176, A:C.182, A:C.220, A:C.224 SF4.3: 11 residues within 4Å: Chain A: C.267, P.268, T.269, I.272, I.281, C.286, V.287, R.288, C.289, M.290, C.292 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.267, A:C.286, A:C.289, A:C.292 SF4.5: 10 residues within 4Å: Chain B: T.134, Q.135, C.140, T.142, P.143, C.177, C.178, N.180, C.182 Ligands: SRM.1 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.140, B:C.178, B:C.182 SF4.6: 11 residues within 4Å: Chain B: C.220, P.221, T.222, L.225, C.241, M.242, Y.243, C.244, G.245, C.247, L.256 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.220, B:C.241, B:C.244, B:C.247 SF4.9: 10 residues within 4Å: Chain C: C.176, M.177, C.182, F.184, A.185, G.219, C.220, N.222, D.223, C.224 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.176, C:C.182, C:C.220, C:C.224, H2O.21 SF4.10: 11 residues within 4Å: Chain C: C.267, P.268, T.269, A.271, I.272, C.286, V.287, R.288, C.289, M.290, C.292 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.267, C:C.286, C:C.289, C:C.292 SF4.11: 10 residues within 4Å: Chain D: T.134, Q.135, C.140, T.142, P.143, C.177, C.178, N.180, C.182 Ligands: SRM.8 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.134, D:C.140, D:C.178, D:C.182, H2O.21 SF4.12: 12 residues within 4Å: Chain D: C.220, P.221, T.222, L.225, C.241, M.242, Y.243, C.244, G.245, N.246, C.247, L.256 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.220, D:C.241, D:C.244, D:C.247

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: R.99, R.171, K.212, K.214 Ligands: SRM.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.99, A:R.99, A:R.171, A:R.171, A:K.212, A:K.214, A:K.214 Water bridges: A:T.134, A:T.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiffer, A. et al., Structure of the dissimilatory sulfite reductase from the hyperthermophilic archaeon Archaeoglobus fulgidus. J.Mol.Biol. (2008)

Release Date

2010-05-12

Peptides

Sulfite reductase, dissimilatory-type subunit alpha: AC
Sulfite reductase, dissimilatory-type subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

B
B

D
E

Sulfite reductase, dissimilatory-type subunit alpha

Sulfite reductase, dissimilatory-type subunit beta

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