SMTL ID : 6tge.2 (7 other biounits)

NADP dependent methylene-tetrahydromethanopterin dehydrogenase-NADP+-methenyl-H4MPT+ complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

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

H4M.1: 20 residues within 4Å: Chain A: S.16, F.18, D.19, N.97, G.98, T.102, I.199, A.223, L.250, G.253, K.256, L.257 Chain C: Y.51, T.52, G.54, G.55, K.58, P.87, F.88 Ligands: NAP.2 23 PLIP interactions: 16 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:I.199, A:A.223, C:Y.51, C:Y.51 Hydrogen bonds: A:S.16, A:S.16, A:T.102, A:L.250, A:K.256, C:Y.51, C:G.55, C:K.58, C:P.87 Water bridges: A:D.19, A:D.95, A:N.97, A:N.97, A:N.97, A:G.254, C:G.54 Salt bridges: A:D.19 pi-Stacking: A:F.18 pi-Cation interactions: A:F.18 H4M.5: 14 residues within 4Å: Chain A: Y.51, G.54, G.55 Chain B: S.16, F.18, D.19, N.97, G.98, L.250, G.253, G.254, K.256, L.257 Ligands: NAP.4 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.257, A:Y.51 Hydrogen bonds: B:S.16, B:S.16, B:L.250, B:K.256 Water bridges: B:D.19, B:D.95, B:N.97, B:A.249, B:G.253, A:G.54 Salt bridges: B:D.19 pi-Stacking: B:F.18 pi-Cation interactions: B:F.18 H4M.7: 12 residues within 4Å: Chain B: Y.51, F.88 Chain C: S.16, F.18, D.19, N.97, G.98, T.235, L.250, G.254, K.256 Ligands: NAP.6 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:Y.51, C:F.18 Hydrogen bonds: B:Y.51, C:S.16, C:S.16, C:K.256 Water bridges: C:D.19, C:N.97, C:K.256 Salt bridges: C:D.19 pi-Stacking: C:F.18

3 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 22 residues within 4Å: Chain A: N.97, T.102, A.127, T.129, G.130, P.131, V.132, G.133, G.151, R.152, K.156, A.196, G.197, A.198, I.199, L.201, Y.221, N.222, A.249, G.253, K.256 Ligands: H4M.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:T.102 Hydrogen bonds: A:N.97, A:T.129, A:V.132, A:G.133, A:R.152, A:K.156, A:G.197, A:A.198, A:Y.221 Water bridges: A:R.152, A:R.152, A:K.153, A:K.153, A:R.183 Salt bridges: A:R.152, A:K.156 pi-Cation interactions: A:R.152, A:R.152 NAP.4: 21 residues within 4Å: Chain B: N.97, T.102, A.127, T.129, G.130, P.131, V.132, G.151, R.152, K.153, K.156, A.196, G.197, A.198, I.199, L.201, L.203, Y.221, N.222, K.256 Ligands: H4M.5 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:T.102 Hydrogen bonds: B:T.129, B:T.129, B:V.132, B:R.152, B:K.156, B:G.197, B:A.198 Water bridges: B:N.97, B:N.97, B:N.97, B:N.97, B:A.127, B:T.129, B:G.133, B:R.152, B:K.153, B:K.153, B:R.183, B:I.199, B:Y.221, B:Y.221, B:A.223, B:A.249, B:A.249, B:G.253 Salt bridges: B:R.152, B:K.153, B:K.156 pi-Cation interactions: B:R.152, B:R.152 NAP.6: 19 residues within 4Å: Chain C: N.97, T.102, A.127, T.129, G.130, P.131, V.132, G.151, R.152, K.156, A.196, G.197, A.198, I.199, L.201, Y.221, N.222, K.256 Ligands: H4M.7 24 PLIP interactions: 24 interactions with chain C Hydrogen bonds: C:T.102, C:T.129, C:V.132, C:R.152, C:K.156, C:G.197, C:A.198 Water bridges: C:N.97, C:N.97, C:N.97, C:T.129, C:G.133, C:R.152, C:R.152, C:K.153, C:K.153, C:K.153, C:K.153, C:R.183, C:A.223 Salt bridges: C:R.152, C:K.156 pi-Cation interactions: C:R.152, C:R.152

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

SO4.3: 10 residues within 4Å: Chain A: Y.24, H.30, I.31 Chain B: Y.24, D.29, H.30, I.31 Chain C: Y.24, H.30, I.31 8 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: B:Y.24, C:Y.24, C:I.31, A:Y.24, A:I.31 Salt bridges: B:H.30, C:H.30, A:H.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, G. et al., The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase. J.Mol.Biol. (2020)

Release Date

2020-02-26

Peptides

Bifunctional NADP-dependent methylenetetrahydromethanopterin dehydrogenase/methylenetetrahydrofolate dehydrogenase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Bifunctional NADP-dependent methylenetetrahydromethanopterin dehydrogenase/methylenetetrahydrofolate dehydrogenase

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