SMTL ID : 3iqe.1

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methylene-tetrahydromethanopterin and coenzyme F420

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

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

H4M.1: 20 residues within 4Å: Chain A: N.13, L.14, G.15, V.42, A.123, M.124, L.125, A.127, R.128, R.129, E.130, M.137, N.141, L.144, C.221, Y.230 Chain D: E.26, R.27, A.28 Ligands: F42.2 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:V.42, A:A.127, D:A.28 Hydrogen bonds: A:N.13, A:A.123, A:L.125, A:A.127, A:R.128, A:R.129, A:N.141, A:N.141, A:Y.230, D:R.27 Water bridges: A:G.15, A:G.15 Salt bridges: A:R.128, A:R.129 H4M.3: 20 residues within 4Å: Chain B: N.13, L.14, G.15, V.42, A.123, M.124, L.125, A.127, R.128, R.129, E.130, M.137, N.141, L.144, C.221, Y.230 Chain F: E.26, R.27, A.28 Ligands: F42.4 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:V.42, B:A.127, F:A.28 Hydrogen bonds: B:N.13, B:A.123, B:L.125, B:R.128, B:R.129, B:R.129, B:E.130, B:N.141, B:N.141, B:C.221, B:Y.230, F:R.27 Water bridges: B:R.129, B:Y.230 Salt bridges: B:R.128 H4M.7: 20 residues within 4Å: Chain C: N.13, L.14, G.15, V.42, M.124, L.125, A.127, R.128, R.129, E.130, M.137, N.141, L.144, C.221, F.222, Y.230 Chain E: E.26, R.27, A.28 Ligands: F42.8 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:V.42, C:A.127, C:F.222, E:A.28 Hydrogen bonds: C:N.13, C:A.123, C:L.125, C:R.128, C:R.129, C:R.129, C:E.130, C:N.141, C:N.141, C:C.221, C:Y.230, E:R.27 Water bridges: C:G.15, C:R.129 Salt bridges: C:R.128 H4M.11: 21 residues within 4Å: Chain A: E.26, R.27, A.28 Chain D: N.13, L.14, G.15, V.42, A.123, M.124, L.125, A.127, R.128, R.129, E.130, M.137, N.141, L.144, C.221, F.222, Y.230 Ligands: F42.12 18 PLIP interactions: 16 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:V.42, D:A.127, D:F.222, A:A.28 Hydrogen bonds: D:N.13, D:G.15, D:A.123, D:L.125, D:R.128, D:R.129, D:R.129, D:E.130, D:N.141, D:N.141, D:C.221, D:Y.230, A:R.27 Salt bridges: D:R.128 H4M.15: 20 residues within 4Å: Chain C: E.26, R.27, A.28 Chain E: N.13, L.14, G.15, V.42, M.124, L.125, A.127, R.128, R.129, E.130, M.137, N.141, L.144, C.221, F.222, Y.230 Ligands: F42.16 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:V.42, E:A.127, E:F.222, C:A.28 Hydrogen bonds: E:N.13, E:G.15, E:A.123, E:L.125, E:R.129, E:R.129, E:E.130, E:N.141, E:N.141, E:C.221, C:R.27 Salt bridges: E:R.128 H4M.18: 20 residues within 4Å: Chain B: E.26, R.27, A.28 Chain F: N.13, L.14, G.15, V.42, M.124, L.125, A.127, R.128, R.129, E.130, M.137, N.141, L.144, C.221, F.222, Y.230 Ligands: F42.19 19 PLIP interactions: 2 interactions with chain B, 17 interactions with chain F Hydrophobic interactions: B:A.28, F:V.42, F:A.127, F:F.222 Hydrogen bonds: B:R.27, F:N.13, F:A.123, F:L.125, F:R.128, F:R.129, F:E.130, F:N.141, F:N.141, F:C.221 Water bridges: F:G.15, F:G.15, F:R.129 Salt bridges: F:R.128, F:R.129

6 x F42: COENZYME F420(Non-covalent)

F42.2: 14 residues within 4Å: Chain A: G.12, N.13, L.14, V.42, M.44, P.73, N.74, D.99, P.101, K.104, M.124, F.222 Chain D: A.28 Ligands: H4M.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.14, A:P.73, A:P.73, A:M.124 Hydrogen bonds: A:N.13, A:V.42, A:N.74, A:D.99 Water bridges: A:M.44 Salt bridges: A:K.104 F42.4: 13 residues within 4Å: Chain B: G.12, N.13, L.14, V.42, M.44, P.73, N.74, D.99, P.101, M.124, F.222 Chain F: A.28 Ligands: H4M.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.14, B:P.73, B:P.73, B:M.124 Hydrogen bonds: B:N.13, B:V.42, B:N.74, B:D.99 Water bridges: B:M.124 F42.8: 13 residues within 4Å: Chain C: G.12, N.13, L.14, V.42, M.44, P.73, N.74, D.99, P.101, M.124, F.222 Chain E: A.28 Ligands: H4M.7 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.14, C:P.73, C:P.73, C:M.124 Hydrogen bonds: C:N.13, C:V.42, C:N.74, C:D.99 Water bridges: C:M.44, C:M.124 Salt bridges: C:K.104 F42.12: 13 residues within 4Å: Chain A: A.28 Chain D: G.12, N.13, L.14, V.42, M.44, P.73, N.74, D.99, P.101, M.124, F.222 Ligands: H4M.11 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.14, D:P.73, D:P.73, D:M.124 Hydrogen bonds: D:N.13, D:V.42, D:N.74, D:D.99 Water bridges: D:M.44, D:D.99 F42.16: 12 residues within 4Å: Chain C: A.28 Chain E: G.12, N.13, L.14, V.42, M.44, P.73, N.74, D.99, P.101, M.124 Ligands: H4M.15 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:L.14, E:P.73, E:P.73, E:M.124 Hydrogen bonds: E:N.13, E:V.42, E:N.74, E:D.99 Water bridges: E:M.44, E:M.124 F42.19: 13 residues within 4Å: Chain B: A.28 Chain F: G.12, N.13, L.14, V.42, M.44, P.73, N.74, D.99, P.101, M.124, F.222 Ligands: H4M.18 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:L.14, F:P.73, F:P.73, F:M.124 Hydrogen bonds: F:N.13, F:V.42, F:N.74, F:D.99 Water bridges: F:M.44, F:M.124 Salt bridges: F:K.104

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 2 residues within 4Å: Chain B: E.85, D.89 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.85, B:D.89, B:D.89 CA.6: 2 residues within 4Å: Chain B: E.34, R.36 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.34, B:E.34 CA.9: 3 residues within 4Å: Chain C: K.227, E.228 Chain E: M.279 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.228, H2O.20, H2O.20 CA.13: 2 residues within 4Å: Chain D: E.50, E.54 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.50, D:E.54, H2O.16

3 x NA: SODIUM ION(Non-functional Binders)

NA.10: 2 residues within 4Å: Chain C: D.215 Chain F: N.212 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain C Water bridges: F:N.212 Hydrogen bonds: C:D.215, C:D.215 NA.14: 5 residues within 4Å: Chain D: D.25, E.26, R.27, A.28, D.29 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.27, D:D.29, D:D.29 NA.17: 1 residues within 4Å: Chain E: D.66 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ceh, K. et al., Structural basis of the hydride transfer mechanism in F(420)-dependent methylenetetrahydromethanopterin dehydrogenase. Biochemistry (2009)

Release Date

2009-10-06

Peptides

F420-dependent methylenetetrahydromethanopterin dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

F420-dependent methylenetetrahydromethanopterin dehydrogenase

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