SMTL ID : 6hux.1

HmdII from Methanocaldococcus jannaschii reconstitued with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydromethanopterin at 2.5 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

18 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 2 residues within 4Å: Chain A: G.36, G.37 Ligand excluded by PLIP ACT.2: 3 residues within 4Å: Chain A: A.200, Y.201, V.202 Ligand excluded by PLIP ACT.3: 5 residues within 4Å: Chain A: P.163, H.165, G.166, G.197, K.198 Ligand excluded by PLIP ACT.4: 1 residues within 4Å: Chain A: S.358 Ligand excluded by PLIP ACT.5: 6 residues within 4Å: Chain A: P.317, T.318, T.319 Chain B: D.176, Q.324, K.331 Ligand excluded by PLIP ACT.6: 3 residues within 4Å: Chain A: S.359, S.360, V.361 Ligand excluded by PLIP ACT.7: 3 residues within 4Å: Chain A: F.102, G.103, K.104 Ligand excluded by PLIP ACT.8: 4 residues within 4Å: Chain A: K.13, K.91, H.92 Ligands: SO4.18 Ligand excluded by PLIP ACT.9: 1 residues within 4Å: Chain A: K.269 Ligand excluded by PLIP ACT.25: 2 residues within 4Å: Chain B: G.36, G.37 Ligand excluded by PLIP ACT.26: 3 residues within 4Å: Chain B: A.200, Y.201, V.202 Ligand excluded by PLIP ACT.27: 5 residues within 4Å: Chain B: P.163, H.165, G.166, G.197, K.198 Ligand excluded by PLIP ACT.28: 1 residues within 4Å: Chain B: S.358 Ligand excluded by PLIP ACT.29: 6 residues within 4Å: Chain A: D.176, Q.324, K.331 Chain B: P.317, T.318, T.319 Ligand excluded by PLIP ACT.30: 3 residues within 4Å: Chain B: S.359, S.360, V.361 Ligand excluded by PLIP ACT.31: 3 residues within 4Å: Chain B: F.102, G.103, K.104 Ligand excluded by PLIP ACT.32: 4 residues within 4Å: Chain B: K.13, K.91, H.92 Ligands: SO4.42 Ligand excluded by PLIP ACT.33: 1 residues within 4Å: Chain B: K.269 Ligand excluded by PLIP

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

FE9.10: 27 residues within 4Å: Chain A: Y.17, G.18, A.19, G.20, N.21, L.24, Y.25, A.60, E.61, P.62, I.66, D.86, F.99, T.100, P.101, R.108, I.109, T.126, C.127, T.128, H.155, P.156, A.157, A.158, V.159, P.160 Ligands: E4M.12 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:L.24, A:F.99, A:F.99, A:F.99, A:T.128 Hydrogen bonds: A:G.18, A:A.19, A:G.20, A:G.20, A:N.21, A:Y.25, A:A.60, A:R.108, A:R.108, A:C.127, A:A.157, A:A.158 Water bridges: A:F.102 Salt bridges: A:E.61, A:D.86 Metal complexes: A:C.127 FE9.34: 27 residues within 4Å: Chain B: Y.17, G.18, A.19, G.20, N.21, L.24, Y.25, A.60, E.61, P.62, I.66, D.86, F.99, T.100, P.101, R.108, I.109, T.126, C.127, T.128, H.155, P.156, A.157, A.158, V.159, P.160 Ligands: E4M.36 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:L.24, B:F.99, B:F.99, B:F.99, B:T.128 Hydrogen bonds: B:G.18, B:A.19, B:G.20, B:G.20, B:N.21, B:Y.25, B:A.60, B:R.108, B:R.108, B:C.127, B:A.157, B:A.158 Water bridges: B:F.102 Salt bridges: B:E.61, B:D.86 Metal complexes: B:C.127

2 x NA: SODIUM ION(Non-functional Binders)

NA.11: 3 residues within 4Å: Chain A: D.86, R.108, T.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.86, A:D.86, A:R.108 NA.35: 3 residues within 4Å: Chain B: D.86, R.108, T.112 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.86, B:R.108, B:T.112

2 x E4M: 1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol(Non-covalent)

E4M.12: 17 residues within 4Å: Chain A: L.24, Y.25, L.29, F.102, C.127, A.157, V.159, A.212, D.213, M.214, S.216 Chain B: I.237, N.238, S.279, S.282, M.283 Ligands: FE9.10 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.24, A:Y.25, A:L.29, A:F.102, A:V.159, B:I.237, B:I.237 Hydrogen bonds: A:A.212, A:M.214, A:S.216, B:S.279, B:S.282 Water bridges: B:N.238 E4M.36: 17 residues within 4Å: Chain A: I.237, N.238, S.279, S.282, M.283 Chain B: L.24, Y.25, L.29, F.102, C.127, A.157, V.159, A.212, D.213, M.214, S.216 Ligands: FE9.34 13 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:I.237, A:I.237, B:L.24, B:Y.25, B:L.29, B:F.102, B:V.159 Hydrogen bonds: A:S.279, A:S.282, B:A.212, B:M.214, B:S.216 Water bridges: A:N.238

2 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 3 residues within 4Å: Chain A: I.264, E.265 Chain B: E.245 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:E.265, A:E.265, B:E.245 MG.37: 3 residues within 4Å: Chain A: E.245 Chain B: I.264, E.265 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.245, B:E.265, B:E.265

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

SO4.14: 4 residues within 4Å: Chain A: R.345, R.348, P.356, N.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.357 Salt bridges: A:R.345, A:R.348 SO4.15: 4 residues within 4Å: Chain A: R.345, K.349 Chain B: S.325, K.328 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:E.260 Salt bridges: A:R.345, A:K.349, B:K.328 SO4.16: 1 residues within 4Å: Chain A: K.145 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.145 SO4.17: 2 residues within 4Å: Chain A: K.91, H.116 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.91, A:H.116 SO4.18: 5 residues within 4Å: Chain A: K.13, K.91, H.92, P.118 Ligands: ACT.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.91 Salt bridges: A:K.13 SO4.19: 6 residues within 4Å: Chain A: T.318, T.319, L.320 Chain B: D.206, A.347, F.351 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.320, A:L.320 SO4.20: 3 residues within 4Å: Chain A: R.45, E.49, E.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.49, A:E.52 Salt bridges: A:R.45 SO4.38: 4 residues within 4Å: Chain B: R.345, R.348, P.356, N.357 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.357 Salt bridges: B:R.345, B:R.348 SO4.39: 4 residues within 4Å: Chain A: S.325, K.328 Chain B: R.345, K.349 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.345, B:K.349, A:K.328 SO4.40: 1 residues within 4Å: Chain B: K.145 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.145 SO4.41: 2 residues within 4Å: Chain B: K.91, H.116 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.91, B:H.116 SO4.42: 5 residues within 4Å: Chain B: K.13, K.91, H.92, P.118 Ligands: ACT.32 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.91 Salt bridges: B:K.13 SO4.43: 6 residues within 4Å: Chain A: D.206, A.347, F.351 Chain B: T.318, T.319, L.320 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.206, B:L.320, B:L.320 SO4.44: 3 residues within 4Å: Chain B: R.45, E.49, E.52 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.52 Salt bridges: B:R.45

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.21: 5 residues within 4Å: Chain A: G.172, K.173, V.202, V.203, P.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.173, A:K.173 EDO.22: 2 residues within 4Å: Chain A: R.143, K.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.143, A:R.143, A:K.178 EDO.23: 3 residues within 4Å: Chain A: T.182, E.183, E.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.183, A:E.184 EDO.45: 5 residues within 4Å: Chain B: G.172, K.173, V.202, V.203, P.204 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.173, B:K.173 EDO.46: 2 residues within 4Å: Chain B: R.143, K.178 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.143, B:R.143, B:K.178 EDO.47: 3 residues within 4Å: Chain B: T.182, E.183, E.184 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.183, B:E.184

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.48: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, T. et al., The Bacterial [Fe]-Hydrogenase Paralog HmdII Uses Tetrahydrofolate Derivatives as Substrates. Angew. Chem. Int. Ed. Engl. (2019)

Release Date

2019-01-09

Peptides

H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338

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