SMTL ID : 6tlk.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

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

NAP.1: 19 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 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: 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:N.97, A:G.130, A:G.133, A:R.152, A:R.152, A:R.152, A:K.153, A:Q.224, A:K.256 Salt bridges: A:R.152, A:K.156 pi-Cation interactions: A:R.152, A:R.152 NAP.4: 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: GOL.5 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: 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:T.129, B:G.133, B:K.153, B:K.153, B:K.153, B:I.199, B:Q.224, B:A.249, B:A.249 Salt bridges: B:R.152, B:K.156 pi-Cation interactions: B:R.152, B:R.152 NAP.11: 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, L.203, Y.221, N.222 Ligands: GOL.13 23 PLIP interactions: 23 interactions with chain C Hydrogen bonds: 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:G.130, C:G.133, C:K.153, C:K.153, C:K.153, C:K.153, C:R.183, C:Q.224, C:K.256, C:K.256 Salt bridges: C:R.152, C:K.156 pi-Cation interactions: C:R.152, C:R.152

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

FMT.2: 3 residues within 4Å: Chain A: A.113, A.114, E.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.216 FMT.6: 4 residues within 4Å: Chain B: T.11, V.37, T.38, A.72 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.11 FMT.7: 3 residues within 4Å: Chain B: Y.51, R.53, G.54 No protein-ligand interaction detected (PLIP) FMT.8: 4 residues within 4Å: Chain B: S.2, K.3, K.4, D.29 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.2 Water bridges: B:K.3, B:K.4 FMT.9: 1 residues within 4Å: Chain B: V.274 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.274 FMT.10: 3 residues within 4Å: Chain B: F.168, K.169, E.278 No protein-ligand interaction detected (PLIP) FMT.16: 2 residues within 4Å: Chain C: K.188, N.211 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.188 FMT.17: 3 residues within 4Å: Chain C: L.109, K.237, L.255 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.237 FMT.18: 2 residues within 4Å: Chain C: K.166, R.167 No protein-ligand interaction detected (PLIP)

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

CL.3: 5 residues within 4Å: Chain A: Y.24, H.30 Chain B: Y.24, H.30 Chain C: H.30 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain B: S.16, F.18, D.19, N.97, G.98, K.256 Ligands: NAP.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.16, B:D.19, B:N.97, B:K.256, B:K.256 Water bridges: B:G.67, B:G.98, B:G.98 GOL.13: 6 residues within 4Å: Chain C: F.18, D.19, N.97, G.98, K.256 Ligands: NAP.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.19, C:K.256 Water bridges: C:G.98, C:G.98 GOL.14: 3 residues within 4Å: Chain A: A.223, L.250 Chain C: Y.51 No protein-ligand interaction detected (PLIP) GOL.15: 1 residues within 4Å: Chain C: F.85 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.224

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.12: 0 residues within 4Å: (No contacts) 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
D

B
E

C
F

Bifunctional protein MdtA

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