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