SMTL ID : 3iqz.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

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

H4M.1: 18 residues within 4Å: Chain A: N.13, L.14, G.15, 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 D: E.26, R.27, A.28 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:A.127, A:F.222, D:A.28 Hydrogen bonds: A:N.13, A:L.125, A:R.128, A:R.129, A:R.129, A:E.130, A:E.130, A:N.141, A:N.141, A:C.221, A:Y.230, D:R.27 Water bridges: A:G.15, A:G.15 Salt bridges: A:R.128 H4M.2: 19 residues within 4Å: Chain B: 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 F: E.26, R.27, A.28 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:V.42, B:A.127, B:F.222, F:A.28 Hydrogen bonds: B:N.13, B:L.125, B:R.128, B:R.129, B:E.130, B:N.141, B:N.141, B:C.221, B:Y.230, F:R.27 Water bridges: B:G.15, B:G.15 Salt bridges: B:R.128, B:R.129 H4M.5: 18 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, Y.230 Chain E: E.26, R.27, A.28 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:V.42, C:A.127, E:A.28 Hydrogen bonds: C:N.13, C:L.125, C:R.128, C:R.129, C:N.141, C:N.141, C:C.221, C:Y.230, C:Y.230, E:R.27 Water bridges: C:G.15, C:G.15, C:R.129, C:R.129 Salt bridges: C:R.128 H4M.6: 18 residues within 4Å: Chain A: E.26, R.27, A.28 Chain D: N.13, L.14, G.15, A.123, M.124, L.125, A.127, R.128, R.129, E.130, M.137, N.141, L.144, C.221, Y.230 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:A.127, A:A.28 Hydrogen bonds: D:N.13, D:G.15, D:A.123, D:L.125, D:R.128, D:R.129, D:E.130, D:N.141, D:N.141, D:C.221, D:Y.230, A:R.27 Water bridges: D:R.129, D:R.129 Salt bridges: D:R.128 H4M.8: 20 residues within 4Å: Chain C: E.26, R.27, A.28 Chain E: 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 17 PLIP interactions: 15 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:A.123, E:L.125, E:R.128, E:R.129, E:R.129, E:E.130, E:N.141, E:N.141, E:C.221, C:R.27 Water bridges: E:G.15 Salt bridges: E:R.128 H4M.10: 18 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, Y.230 17 PLIP interactions: 15 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:V.42, F:A.127, B:A.28 Hydrogen bonds: 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, B:R.27 Water bridges: F:G.15, F:R.129, F:R.129 Salt bridges: F:R.128

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain B: E.111, Q.112, G.113, E.175 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.111

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

NA.7: 5 residues within 4Å: Chain A: K.256, R.263 Chain B: Y.198 Chain D: F.131, E.136 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.263, A:R.263, D:E.136 Water bridges: A:R.252, D:E.239 NA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.11: 1 residues within 4Å: Chain F: R.129 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.129

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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