SMTL ID : 6tlk.1 (1 other biounit)

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene-H4MPT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

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

NAP.1: 20 residues within 4Å: Chain A: 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, L.203, Y.221, N.222, K.256 Ligands: H4M.4 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:V.132 Hydrogen bonds: A:T.102, A:T.129, A:V.132, A:R.152, A:K.156, A:G.197, A:A.198 Water bridges: A:N.97, A:N.97, A:A.127, A:T.129, A:G.130, A:G.133, A:R.152, A:R.152, A:K.153, A:K.153, A:K.153, A:R.183, A:Y.221, A:Y.221, A:Q.224, A:A.249, A:A.249 Salt bridges: A:R.152, A:K.156 pi-Cation interactions: A:R.152, A:R.152 NAP.5: 20 residues within 4Å: Chain B: 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, L.203, Y.221, N.222, K.256 Ligands: H4M.6 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:T.102, B:V.132 Hydrogen bonds: 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:T.129, B:G.130, B:G.133, B:R.152, B:R.152, B:K.153, B:K.153, B:K.153, B:K.153, B:Y.221, B:A.223, B:A.223, B:A.249, B:A.249 Salt bridges: B:R.152, B:K.156 pi-Cation interactions: B:R.152, B:R.152 NAP.7: 20 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, L.203, Y.221, N.222, K.256 Ligands: GOL.8 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:V.132 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:A.127, C:T.129, C:G.130, C:G.133, C:R.152, C:I.199 Salt bridges: C:R.152, C:K.156 pi-Cation interactions: C:R.152, C:R.152

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 2 residues within 4Å: Chain A: K.166, R.167 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.167 FMT.3: 3 residues within 4Å: Chain A: F.85, G.86, R.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.86, A:R.89 Water bridges: A:R.89 FMT.10: 1 residues within 4Å: Chain C: G.68 4 PLIP interactions: 4 interactions with chain C Water bridges: C:D.69, C:N.97, C:N.97, C:N.97 FMT.11: 4 residues within 4Å: Chain C: V.111, K.112, G.116, K.285 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.285

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

H4M.4: 15 residues within 4Å: Chain A: S.16, F.18, D.19, N.97, G.98, T.235, L.250, G.251, G.253, G.254, K.256, L.257 Chain C: Y.51 Ligands: NAP.1, GOL.9 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.257, C:Y.51 Hydrogen bonds: A:S.16, A:S.16, A:N.97, A:L.250, A:K.256 Water bridges: A:N.97, A:G.98, A:G.98, A:A.249, A:G.254, C:Y.51 Salt bridges: A:D.19 pi-Stacking: A:F.18 H4M.6: 13 residues within 4Å: Chain A: Y.51 Chain B: S.16, F.18, D.19, N.97, G.98, T.235, L.250, G.253, G.254, K.256, L.257 Ligands: NAP.5 13 PLIP interactions: 1 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:Y.51, B:L.250 Hydrogen bonds: B:S.16, B:S.16, B:L.250, B:K.256 Water bridges: B:N.97, B:G.98, B:G.98, B:A.249, B:G.254 Salt bridges: B:D.19 pi-Stacking: B:F.18

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain C: F.18, D.19, N.97, G.98, K.256 Ligands: NAP.7 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.19, C:K.256, C:K.256 Water bridges: C:S.16, C:N.97, C:G.98 GOL.9: 4 residues within 4Å: Chain A: L.250 Chain C: Y.51, F.88 Ligands: H4M.4 No protein-ligand interaction detected (PLIP)

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 protein MdtA: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Bifunctional protein MdtA

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