SMTL ID : 6tm3.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.08 Å

Oligo State

homo-trimer

Ligands

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

NAP.1: 24 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, L.203, Y.221, N.222, A.249, G.253, K.256 Ligands: H4M.3, EDO.13 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:T.102 Hydrogen bonds: A:N.97, A:T.129, A:T.129, A:G.130, 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:K.153, A:R.183, A:R.183 Salt bridges: A:R.152, A:K.156 pi-Cation interactions: A:R.152, A:R.152 NAP.20: 24 residues within 4Å: Chain B: 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, L.203, Y.221, N.222, A.249, G.253, K.256 Ligands: H4M.22, EDO.32 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:T.102 Hydrogen bonds: B:N.97, B:T.129, B:T.129, B:G.130, B:V.132, B:G.133, B:R.152, B:K.156, B:G.197, B:A.198, B:Y.221 Water bridges: B:R.152, B:R.152, B:K.153, B:K.153, B:K.153, B:R.183, B:R.183 Salt bridges: B:R.152, B:K.156 pi-Cation interactions: B:R.152, B:R.152 NAP.39: 24 residues within 4Å: Chain C: 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, L.203, Y.221, N.222, A.249, G.253, K.256 Ligands: H4M.41, EDO.51 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:T.102 Hydrogen bonds: C:N.97, C:T.129, C:T.129, C:G.130, C:V.132, C:G.133, C:R.152, C:K.156, C:G.197, C:A.198, C:Y.221 Water bridges: C:R.152, C:R.152, C:K.153, C:K.153, C:K.153, C:R.183, C:R.183 Salt bridges: C:R.152, C:K.156 pi-Cation interactions: C:R.152, C:R.152

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: Q.158, A.161, D.162, N.165, N.171, V.172 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.158, A:Q.158, A:N.165, A:V.172 Water bridges: A:A.174 GOL.21: 6 residues within 4Å: Chain B: Q.158, A.161, D.162, N.165, N.171, V.172 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.158, B:Q.158, B:D.162, B:N.165, B:V.172 Water bridges: B:A.174 GOL.40: 6 residues within 4Å: Chain C: Q.158, A.161, D.162, N.165, N.171, V.172 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.158, C:Q.158, C:N.165, C:V.172 Water bridges: C:A.174

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

H4M.3: 19 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: D.47, Y.51, T.52, R.53, G.54 Ligands: NAP.1, EDO.42 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:I.199, A:A.223, C:D.47, C:Y.51, C:Y.51 Hydrogen bonds: A:S.16, A:S.16, A:N.97, A:T.102, A:K.256, A:K.256, C:Y.51, C:T.52 Water bridges: A:N.97, A:L.250 Salt bridges: A:D.19 pi-Stacking: A:F.18 H4M.22: 19 residues within 4Å: Chain A: D.47, Y.51, T.52, R.53, G.54 Chain B: S.16, F.18, D.19, N.97, G.98, T.102, I.199, A.223, L.250, G.253, K.256, L.257 Ligands: EDO.4, NAP.20 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.199, B:A.223, A:D.47, A:Y.51, A:Y.51 Hydrogen bonds: B:S.16, B:S.16, B:N.97, B:K.256, B:K.256, A:Y.51, A:T.52 Water bridges: B:N.97, B:L.250 Salt bridges: B:D.19 pi-Stacking: B:F.18 H4M.41: 19 residues within 4Å: Chain B: D.47, Y.51, T.52, R.53, G.54 Chain C: S.16, F.18, D.19, N.97, G.98, T.102, I.199, A.223, L.250, G.253, K.256, L.257 Ligands: EDO.23, NAP.39 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:I.199, C:A.223, B:D.47, B:Y.51, B:Y.51 Hydrogen bonds: C:S.16, C:S.16, C:N.97, C:K.256, C:K.256, B:Y.51, B:T.52 Water bridges: C:N.97, C:L.250 Salt bridges: C:D.19 pi-Stacking: C:F.18

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

EDO.4: 5 residues within 4Å: Chain A: A.44 Chain B: S.16, F.18, N.97 Ligands: H4M.22 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: A.138, L.139, G.142, F.168, E.278 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: G.68, D.69, T.129, G.130 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: E.279, K.282, L.283 Ligands: EDO.17 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: Y.241, G.242, G.243, K.244 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: K.119, K.121 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: F.85 Chain B: Q.224, P.225 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: P.39, D.40, A.79, K.82 Ligands: EDO.16 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: K.3, D.29, H.30 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: R.152 Ligands: NAP.1 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: R.83 Chain B: I.199, Q.224 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: A.223, L.227, A.234, L.250 Chain C: F.85, F.88 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: P.39, D.40, A.79, K.82 Ligands: EDO.11 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: G.273, V.274, F.275 Ligands: EDO.7 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: A.44 Chain C: S.16, F.18, N.97 Ligands: H4M.41 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: A.138, L.139, G.142, F.168, E.278 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: G.68, D.69, T.129, G.130 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: E.279, K.282, L.283 Ligands: EDO.36 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: Y.241, G.242, G.243, K.244 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain B: K.119, K.121 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: F.85 Chain C: Q.224, P.225 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: P.39, D.40, A.79, K.82 Ligands: EDO.35 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: K.3, D.29, H.30 Ligand excluded by PLIP EDO.32: 2 residues within 4Å: Chain B: R.152 Ligands: NAP.20 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain B: R.83 Chain C: I.199, Q.224 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain A: F.85, F.88 Chain B: A.223, L.227, A.234, L.250 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain B: P.39, D.40, A.79, K.82 Ligands: EDO.30 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain B: G.273, V.274, F.275 Ligands: EDO.26 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain A: S.16, F.18, N.97 Chain C: A.44 Ligands: H4M.3 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain C: A.138, L.139, G.142, F.168, E.278 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain C: G.68, D.69, T.129, G.130 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain C: E.279, K.282, L.283 Ligands: EDO.55 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain C: Y.241, G.242, G.243, K.244 Ligand excluded by PLIP EDO.47: 2 residues within 4Å: Chain C: K.119, K.121 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain A: Q.224, P.225 Chain C: F.85 Ligand excluded by PLIP EDO.49: 5 residues within 4Å: Chain C: P.39, D.40, A.79, K.82 Ligands: EDO.54 Ligand excluded by PLIP EDO.50: 3 residues within 4Å: Chain C: K.3, D.29, H.30 Ligand excluded by PLIP EDO.51: 2 residues within 4Å: Chain C: R.152 Ligands: NAP.39 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain A: I.199, Q.224 Chain C: R.83 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain B: F.85, F.88 Chain C: A.223, L.227, A.234, L.250 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain C: P.39, D.40, A.79, K.82 Ligands: EDO.49 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain C: G.273, V.274, F.275 Ligands: EDO.45 Ligand excluded by PLIP

6 x LI: LITHIUM ION(Non-covalent)

LI.18: 2 residues within 4Å: Chain A: D.155, Q.158 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, H2O.12 LI.19: 4 residues within 4Å: Chain A: D.180, R.183, L.203, P.205 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.180, A:L.203, H2O.6 LI.37: 2 residues within 4Å: Chain B: D.155, Q.158 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, H2O.31 LI.38: 4 residues within 4Å: Chain B: D.180, R.183, L.203, P.205 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.180, B:L.203, H2O.25 LI.56: 2 residues within 4Å: Chain C: D.155, Q.158 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.155, H2O.50 LI.57: 4 residues within 4Å: Chain C: D.180, R.183, L.203, P.205 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.180, C:L.203, H2O.44

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
A

C
A

Bifunctional protein MdtA

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