SMTL ID : 3h65.1

The Crystal Structure of C176A Mutated [Fe]-Hydrogenase (Hmd) Holoenzyme in Complex with Methylenetetrahydromethanopterin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x I2C: 5'-O-[(S)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxoethyl)pyridin-4-yl]oxy}phosphoryl]guanosine(Non-covalent)

I2C.1: 26 residues within 4Å: Chain A: L.6, G.7, A.8, G.9, C.10, T.13, H.14, S.63, D.64, P.65, P.114, P.115, C.118, D.135, W.148, L.149, P.150, I.158, A.175, A.176, T.177, P.202 Ligands: FE2.2, CMO.3, CMO.4, DTV.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.148, A:T.177 Hydrogen bonds: A:A.8, A:G.9, A:G.9, A:C.10, A:C.10, A:S.63, A:A.176 Water bridges: A:S.133 Salt bridges: A:D.64, A:D.135 I2C.7: 26 residues within 4Å: Chain B: L.6, G.7, A.8, G.9, C.10, T.13, H.14, S.63, D.64, P.65, P.114, P.115, C.118, D.135, W.148, L.149, P.150, I.158, A.175, A.176, T.177, P.202 Ligands: FE2.8, CMO.9, CMO.10, DTV.11 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.148, B:T.177 Hydrogen bonds: B:A.8, B:G.9, B:G.9, B:C.10, B:C.10, B:S.63, B:A.176 Water bridges: B:S.133, B:D.135 Salt bridges: B:D.64, B:D.135

2 x FE2: FE (II) ION(Non-functional Binders)

FE2.2: 4 residues within 4Å: Ligands: I2C.1, CMO.3, CMO.4, DTV.5 2 PLIP interactions: 2 Ligand-Ligand interactions Metal complexes: CMO.3, CMO.4 FE2.8: 4 residues within 4Å: Ligands: I2C.7, CMO.9, CMO.10, DTV.11 2 PLIP interactions: 2 Ligand-Ligand interactions Metal complexes: CMO.9, CMO.10

4 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.3: 9 residues within 4Å: Chain A: H.14, W.148, C.204, V.205, P.206 Ligands: I2C.1, FE2.2, CMO.4, DTV.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.204 CMO.4: 6 residues within 4Å: Chain A: A.176, C.204 Ligands: I2C.1, FE2.2, CMO.3, DTV.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.204 CMO.9: 9 residues within 4Å: Chain B: H.14, W.148, C.204, V.205, P.206 Ligands: I2C.7, FE2.8, CMO.10, DTV.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.204 CMO.10: 6 residues within 4Å: Chain B: A.176, C.204 Ligands: I2C.7, FE2.8, CMO.9, DTV.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.204

2 x DTV: (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Non-covalent)

DTV.5: 7 residues within 4Å: Chain A: T.13, A.17, A.176 Ligands: I2C.1, FE2.2, CMO.3, CMO.4 No protein-ligand interaction detected (PLIP) DTV.11: 7 residues within 4Å: Chain B: T.13, A.17, A.176 Ligands: I2C.7, FE2.8, CMO.9, CMO.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.13

2 x H4M: 5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN(Non-covalent)

H4M.6: 12 residues within 4Å: Chain A: K.151, G.152, C.250, D.251, M.252, S.254 Chain B: L.275, P.278, F.281, T.317, S.320, M.321 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:C.250, A:S.254, B:T.317, B:S.320 Water bridges: A:M.252 Salt bridges: A:K.151 Hydrophobic interactions: B:L.275 H4M.12: 12 residues within 4Å: Chain A: L.275, P.278, F.281, T.317, S.320, M.321 Chain B: K.151, G.152, C.250, D.251, M.252, S.254 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.275 Hydrogen bonds: A:T.317, A:S.320, B:C.250, B:S.254 Water bridges: B:M.252 Salt bridges: B:K.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hiromoto, T. et al., The crystal structure of an [Fe]-hydrogenase-substrate complex reveals the framework for H2 activation. Angew.Chem.Int.Ed.Engl. (2009)

Release Date

2009-09-01

Peptides

5,10-methenyltetrahydromethanopterin hydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5,10-methenyltetrahydromethanopterin hydrogenase

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