SMTL ID : 6ggu.1

Crystal structure of native FE-hydrogenase from Methanothermobacter marburgensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

6 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 7 residues within 4Å: Chain A: F.230, N.239, A.240, Y.241, R.242 Chain E: D.312, K.344 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain E Hydrogen bonds: A:Y.241, A:R.242 Salt bridges: A:R.242, E:D.312, E:K.344 Water bridges: E:D.312, E:D.312, E:K.344 MES.11: 7 residues within 4Å: Chain B: F.230, N.239, A.240, Y.241, R.242 Chain D: D.312, K.344 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain B Water bridges: D:D.312, D:D.312, D:K.344 Salt bridges: D:D.312, D:K.344, B:R.242 Hydrogen bonds: B:Y.241, B:R.242 MES.21: 7 residues within 4Å: Chain C: F.230, N.239, A.240, Y.241, R.242 Chain F: D.312, K.344 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain C Water bridges: F:D.312, F:D.312, F:K.344 Salt bridges: F:D.312, F:K.344, C:R.242 Hydrogen bonds: C:Y.241, C:R.242 MES.31: 7 residues within 4Å: Chain B: D.312, K.344 Chain D: F.230, N.239, A.240, Y.241, R.242 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain B Hydrogen bonds: D:R.242 Salt bridges: D:R.242, B:D.312, B:K.344 Water bridges: B:D.312, B:D.312, B:K.344 MES.41: 7 residues within 4Å: Chain A: D.312, K.344 Chain E: F.230, N.239, A.240, Y.241, R.242 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain E Water bridges: A:D.312, A:D.312, A:K.344 Salt bridges: A:D.312, A:K.344, E:R.242 Hydrogen bonds: E:R.242 MES.51: 7 residues within 4Å: Chain C: D.312, K.344 Chain F: F.230, N.239, A.240, Y.241, R.242 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain F Water bridges: C:D.312, C:D.312, C:K.344 Salt bridges: C:D.312, C:K.344, F:R.242 Hydrogen bonds: F:R.242

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

SO4.2: 3 residues within 4Å: Chain A: Q.285, K.289 Chain E: E.300 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: K.181, K.186 Chain D: K.289 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: K.186, H.187 Chain B: P.175 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: Q.285, K.289 Chain D: E.300 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: K.181, K.186 Chain F: K.289 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain B: K.186, H.187 Chain C: P.175 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain C: Q.285, K.289 Chain F: E.300 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain C: K.181, K.186 Chain E: K.289 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain A: P.175 Chain C: K.186, H.187 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain B: E.300 Chain D: Q.285, K.289 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain A: K.289 Chain D: K.181, K.186 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain D: K.186, H.187 Chain E: P.175 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain A: E.300 Chain E: Q.285, K.289 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain C: K.289 Chain E: K.181, K.186 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain E: K.186, H.187 Chain F: P.175 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain C: E.300 Chain F: Q.285, K.289 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain B: K.289 Chain F: K.181, K.186 Ligand excluded by PLIP SO4.54: 3 residues within 4Å: Chain D: P.175 Chain F: K.186, H.187 Ligand excluded by PLIP

6 x FE9: iron-guanylyl pyridinol cofactor(Non-covalent)

FE9.5: 27 residues within 4Å: Chain A: L.6, G.7, A.8, G.9, C.10, T.13, A.62, D.63, P.64, P.110, P.111, D.131, W.144, F.145, P.146, I.154, A.171, C.172, T.173, H.203, P.204, G.205, A.206, V.207, P.208 Chain C: D.189, V.191 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:W.144, A:W.144, A:W.144, A:A.171, A:T.173 Hydrogen bonds: A:A.8, A:G.9, A:G.9, A:C.10, A:C.10, A:A.62, A:C.172, A:G.205, A:A.206 Water bridges: A:S.42 Salt bridges: A:D.63, A:D.131 pi-Stacking: A:F.145 Metal complexes: A:C.172, C:D.189 FE9.15: 27 residues within 4Å: Chain A: D.189, V.191 Chain B: L.6, G.7, A.8, G.9, C.10, T.13, A.62, D.63, P.64, P.110, P.111, D.131, W.144, F.145, P.146, I.154, A.171, C.172, T.173, H.203, P.204, G.205, A.206, V.207, P.208 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:W.144, B:W.144, B:W.144, B:A.171, B:T.173 Hydrogen bonds: B:A.8, B:G.9, B:G.9, B:C.10, B:C.10, B:A.62, B:C.172, B:G.205, B:A.206 Water bridges: B:S.42 Salt bridges: B:D.63, B:D.131 pi-Stacking: B:F.145 Metal complexes: B:C.172, A:D.189 FE9.25: 27 residues within 4Å: Chain B: D.189, V.191 Chain C: L.6, G.7, A.8, G.9, C.10, T.13, A.62, D.63, P.64, P.110, P.111, D.131, W.144, F.145, P.146, I.154, A.171, C.172, T.173, H.203, P.204, G.205, A.206, V.207, P.208 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:W.144, C:W.144, C:W.144, C:A.171, C:T.173 Hydrogen bonds: C:A.8, C:G.9, C:G.9, C:C.10, C:C.10, C:A.62, C:C.172, C:G.205, C:A.206 Water bridges: C:S.42 Salt bridges: C:D.63, C:D.131 pi-Stacking: C:F.145 Metal complexes: C:C.172, B:D.189 FE9.35: 27 residues within 4Å: Chain D: L.6, G.7, A.8, G.9, C.10, T.13, A.62, D.63, P.64, P.110, P.111, D.131, W.144, F.145, P.146, I.154, A.171, C.172, T.173, H.203, P.204, G.205, A.206, V.207, P.208 Chain F: D.189, V.191 20 PLIP interactions: 19 interactions with chain D, 1 interactions with chain F, Hydrophobic interactions: D:W.144, D:W.144, D:W.144, D:A.171, D:T.173 Hydrogen bonds: D:A.8, D:G.9, D:G.9, D:C.10, D:C.10, D:A.62, D:C.172, D:G.205, D:A.206 Water bridges: D:S.42 Salt bridges: D:D.63, D:D.131 pi-Stacking: D:F.145 Metal complexes: D:C.172, F:D.189 FE9.45: 27 residues within 4Å: Chain D: D.189, V.191 Chain E: L.6, G.7, A.8, G.9, C.10, T.13, A.62, D.63, P.64, P.110, P.111, D.131, W.144, F.145, P.146, I.154, A.171, C.172, T.173, H.203, P.204, G.205, A.206, V.207, P.208 20 PLIP interactions: 19 interactions with chain E, 1 interactions with chain D, Hydrophobic interactions: E:W.144, E:W.144, E:W.144, E:A.171, E:T.173 Hydrogen bonds: E:A.8, E:G.9, E:G.9, E:C.10, E:C.10, E:A.62, E:C.172, E:G.205, E:A.206 Water bridges: E:S.42 Salt bridges: E:D.63, E:D.131 pi-Stacking: E:F.145 Metal complexes: E:C.172, D:D.189 FE9.55: 27 residues within 4Å: Chain E: D.189, V.191 Chain F: L.6, G.7, A.8, G.9, C.10, T.13, A.62, D.63, P.64, P.110, P.111, D.131, W.144, F.145, P.146, I.154, A.171, C.172, T.173, H.203, P.204, G.205, A.206, V.207, P.208 20 PLIP interactions: 19 interactions with chain F, 1 interactions with chain E, Hydrophobic interactions: F:W.144, F:W.144, F:W.144, F:A.171, F:T.173 Hydrogen bonds: F:A.8, F:G.9, F:G.9, F:C.10, F:C.10, F:A.62, F:C.172, F:G.205, F:A.206 Water bridges: F:S.42 Salt bridges: F:D.63, F:D.131 pi-Stacking: F:F.145 Metal complexes: F:C.172, E:D.189

30 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: F.336, E.340 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: S.17, I.19 Chain C: L.190, V.191, K.193 Ligands: GOL.8 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: I.19 Chain E: S.322, F.325 Ligands: GOL.7 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain A: P.35, A.77, Y.78, E.79 Ligand excluded by PLIP GOL.10: 2 residues within 4Å: Chain A: V.276, G.326 Ligand excluded by PLIP GOL.16: 2 residues within 4Å: Chain B: F.336, E.340 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain A: L.190, V.191, K.193 Chain B: S.17, I.19 Ligands: GOL.18 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain B: I.19 Chain D: S.322, F.325 Ligands: GOL.17 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: P.35, A.77, Y.78, E.79 Ligand excluded by PLIP GOL.20: 2 residues within 4Å: Chain B: V.276, G.326 Ligand excluded by PLIP GOL.26: 2 residues within 4Å: Chain C: F.336, E.340 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain B: L.190, V.191, K.193 Chain C: S.17, I.19 Ligands: GOL.28 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain C: I.19 Chain F: S.322, F.325 Ligands: GOL.27 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain C: P.35, A.77, Y.78, E.79 Ligand excluded by PLIP GOL.30: 2 residues within 4Å: Chain C: V.276, G.326 Ligand excluded by PLIP GOL.36: 2 residues within 4Å: Chain D: F.336, E.340 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain D: S.17, I.19 Chain F: L.190, V.191, K.193 Ligands: GOL.38 Ligand excluded by PLIP GOL.38: 4 residues within 4Å: Chain B: S.322, F.325 Chain D: I.19 Ligands: GOL.37 Ligand excluded by PLIP GOL.39: 4 residues within 4Å: Chain D: P.35, A.77, Y.78, E.79 Ligand excluded by PLIP GOL.40: 2 residues within 4Å: Chain D: V.276, G.326 Ligand excluded by PLIP GOL.46: 2 residues within 4Å: Chain E: F.336, E.340 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain D: L.190, V.191, K.193 Chain E: S.17, I.19 Ligands: GOL.48 Ligand excluded by PLIP GOL.48: 4 residues within 4Å: Chain A: S.322, F.325 Chain E: I.19 Ligands: GOL.47 Ligand excluded by PLIP GOL.49: 4 residues within 4Å: Chain E: P.35, A.77, Y.78, E.79 Ligand excluded by PLIP GOL.50: 2 residues within 4Å: Chain E: V.276, G.326 Ligand excluded by PLIP GOL.56: 2 residues within 4Å: Chain F: F.336, E.340 Ligand excluded by PLIP GOL.57: 6 residues within 4Å: Chain E: L.190, V.191, K.193 Chain F: S.17, I.19 Ligands: GOL.58 Ligand excluded by PLIP GOL.58: 4 residues within 4Å: Chain C: S.322, F.325 Chain F: I.19 Ligands: GOL.57 Ligand excluded by PLIP GOL.59: 4 residues within 4Å: Chain F: P.35, A.77, Y.78, E.79 Ligand excluded by PLIP GOL.60: 2 residues within 4Å: Chain F: V.276, G.326 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, T. et al., Self-protection of the catalytic iron center of a methanogenic [Fe]-hydrogenase via a dynamic dimer-to-hexamer transformation. To Be Published

Release Date

2019-05-22

Peptides

5,10-methenyltetrahydromethanopterin hydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

5,10-methenyltetrahydromethanopterin hydrogenase

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