SMTL ID : 2vpw.1

Polysulfide reductase with bound menaquinone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: C.44, G.46, C.47, W.49, R.50, C.51, L.78, C.79, R.81, G.82, H.215, N.216 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.44, A:C.47, A:C.51, A:C.79 SF4.5: 14 residues within 4Å: Chain B: C.13, V.14, G.15, C.16, A.17, A.18, C.19, I.38, P.55, T.134, C.135, T.137, C.139, R.140 5 PLIP interactions: 5 interactions with chain B, Metal complexes: B:C.13, B:C.16, B:C.16, B:C.19, B:C.135 SF4.6: 12 residues within 4Å: Chain B: C.23, N.27, N.35, L.36, Q.57, C.116, T.117, F.118, C.119, P.129, A.130, C.131 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.23, B:C.116, B:C.119, B:C.131 SF4.7: 13 residues within 4Å: Chain B: C.58, L.59, H.60, C.61, P.64, C.66, V.83, C.100, P.101, Y.102, A.104, R.105, K.115 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.58, B:C.61, B:C.66, B:C.100 SF4.8: 11 residues within 4Å: Chain B: C.70, P.71, S.75, C.90, I.91, A.92, C.93, G.94, A.95, C.96, V.113 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.70, B:C.90, B:C.93, B:C.96 SF4.10: 12 residues within 4Å: Chain D: C.44, G.46, C.47, W.49, R.50, C.51, L.78, C.79, R.81, G.82, H.215, N.216 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.44, D:C.47, D:C.51, D:C.79 SF4.14: 14 residues within 4Å: Chain E: C.13, V.14, G.15, C.16, A.17, A.18, C.19, I.38, P.55, C.135, P.136, T.137, C.139, R.140 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.13, E:C.16, E:C.19, E:C.135 SF4.15: 12 residues within 4Å: Chain E: C.23, N.27, N.35, L.36, Q.57, C.116, T.117, F.118, C.119, P.129, A.130, C.131 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.23, E:C.116, E:C.119, E:C.131 SF4.16: 11 residues within 4Å: Chain E: C.58, L.59, H.60, C.61, P.65, C.66, V.83, C.100, P.101, Y.102, R.105 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.58, E:C.61, E:C.66, E:C.100 SF4.17: 12 residues within 4Å: Chain E: C.70, P.71, T.72, V.85, C.90, I.91, A.92, C.93, G.94, A.95, C.96, V.113 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.70, E:C.90, E:C.93, E:C.96

4 x MGD: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE(Non-covalent)(Covalent)

MGD.2: 31 residues within 4Å: Chain A: F.48, H.145, P.168, S.169, L.172, C.173, H.333, Y.438, G.439, I.440, N.441, H.444, S.445, I.465, D.466, Q.470, H.472, E.482, R.488, Y.623, R.625, F.631, A.632, R.633, H.697, D.716, N.717, Q.720, L.734 Ligands: MGD.3, MO.4 31 PLIP interactions: 31 interactions with chain A Hydrogen bonds: A:H.333, A:G.439, A:N.441, A:S.445, A:S.445, A:S.445, A:I.465, A:I.465, A:Q.470, A:H.472, A:R.488, A:R.488, A:R.625, A:R.625, A:A.632, A:R.633, A:R.633, A:N.717, A:Q.720 Water bridges: A:I.440, A:D.466, A:V.467, A:R.633, A:R.633 Salt bridges: A:H.145, A:D.466, A:E.482, A:R.633, A:D.716 pi-Stacking: A:H.697 pi-Cation interactions: A:H.697 MGD.3: 33 residues within 4Å: Chain A: R.81, C.173, I.206, G.207, H.208, H.209, E.212, D.213, T.214, H.215, V.235, D.236, P.237, R.238, I.252, P.254, G.255, D.257, T.331, R.332, H.333, W.336, Y.337, L.622, R.625, S.626, P.627, H.629, T.630, F.631, R.735 Ligands: MGD.2, MO.4 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:H.209, A:H.209, A:D.213, A:D.213, A:T.214, A:V.235, A:V.235, A:R.238, A:R.238, A:G.255, A:T.331, A:R.332, A:H.333, A:H.333, A:H.629, A:F.631, A:R.735 Water bridges: A:D.257, A:R.625, A:S.626, A:R.735 Salt bridges: A:H.209, A:H.209, A:D.236, A:D.257, A:R.735 pi-Stacking: A:W.336 MGD.11: 31 residues within 4Å: Chain D: F.48, H.145, P.168, L.172, C.173, H.333, Y.438, G.439, I.440, N.441, H.444, S.445, I.465, D.466, V.467, Q.470, H.472, E.482, R.488, Y.623, R.625, F.631, A.632, R.633, H.697, D.716, N.717, Q.720, L.734 Ligands: MGD.12, MO.13 29 PLIP interactions: 29 interactions with chain D Hydrogen bonds: D:G.439, D:N.441, D:N.441, D:S.445, D:S.445, D:S.445, D:I.465, D:I.465, D:V.467, D:Q.470, D:R.488, D:R.625, D:R.625, D:A.632, D:R.633, D:R.633, D:N.717, D:Q.720 Water bridges: D:Y.438, D:R.488, D:R.633, D:R.633 Salt bridges: D:H.145, D:D.466, D:E.482, D:R.633, D:D.716 pi-Stacking: D:H.697 pi-Cation interactions: D:H.697 MGD.12: 33 residues within 4Å: Chain D: R.81, C.173, I.206, G.207, H.208, H.209, E.212, D.213, T.214, H.215, V.235, D.236, P.237, R.238, I.252, P.254, G.255, D.257, T.331, R.332, H.333, W.336, Y.337, L.622, R.625, S.626, P.627, H.629, T.630, F.631, R.735 Ligands: MGD.11, MO.13 33 PLIP interactions: 33 interactions with chain D Hydrogen bonds: D:G.207, D:H.208, D:H.209, D:H.209, D:D.213, D:D.213, D:T.214, D:V.235, D:V.235, D:R.238, D:R.238, D:G.255, D:R.332, D:H.333, D:H.333, D:Y.337, D:H.629, D:F.631, D:R.735, D:R.735 Water bridges: D:R.81, D:H.208, D:D.257, D:T.331, D:T.331, D:S.626, D:T.630 Salt bridges: D:H.209, D:H.209, D:D.236, D:D.257, D:R.735 pi-Cation interactions: D:R.81

2 x MO: MOLYBDENUM ATOM(Non-covalent)

MO.4: 3 residues within 4Å: Chain A: C.173 Ligands: MGD.2, MGD.3 Ligand excluded by PLIP MO.13: 3 residues within 4Å: Chain D: C.173 Ligands: MGD.11, MGD.12 Ligand excluded by PLIP

2 x MQ7: MENAQUINONE-7(Non-covalent)

MQ7.9: 10 residues within 4Å: Chain B: I.91, C.93 Chain C: W.14, N.18, H.21, L.64, H.76, L.79, I.89, Y.130 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:I.91, C:L.64, C:L.64, C:L.64, C:L.79, C:I.89, C:I.89 Hydrogen bonds: C:Y.130 MQ7.18: 11 residues within 4Å: Chain E: I.91, C.93 Chain F: N.18, H.21, L.64, W.65, E.67, H.76, L.79, I.89, Y.130 7 PLIP interactions: 1 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: E:I.91, F:L.64, F:L.64, F:L.64, F:L.79, F:I.89 Hydrogen bonds: F:Y.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jormakka, M. et al., Molecular Mechanism of Energy Conservation in Polysulfide Respiration. Nat.Struct.Mol.Biol. (2008)

Release Date

2008-06-10

Peptides

THIOSULFATE REDUCTASE: AD
NRFC PROTEIN: BE
HYPOTHETICAL MEMBRANE SPANNING PROTEIN: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

B
B

E
F

C
C

F
G

Membrane

We predict this structure to be a membrane protein.
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THIOSULFATE REDUCTASE

NRFC PROTEIN

HYPOTHETICAL MEMBRANE SPANNING PROTEIN

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