SMTL ID : 3iqf.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x E4M: 1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol(Non-covalent)

E4M.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, F.222, Y.230 Chain D: E.26, R.27, A.28 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:V.42, A:A.127, A:F.222, D:A.28 Hydrogen bonds: A:N.13, A:G.15, A:A.123, A:L.125, A:R.128, A:R.129, A:R.129, A:N.141, A:N.141, A:C.221, A:Y.230, D:R.27 Water bridges: A:R.129, A:R.129 Salt bridges: A:R.128 E4M.2: 18 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, 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, F:A.28 Hydrogen bonds: B:N.13, B:G.15, B:A.123, B:L.125, B:R.128, B:R.129, B:R.129, B:N.141, B:N.141, B:C.221, B:Y.230, F:R.27 Water bridges: B:R.128, B:R.129 Salt bridges: B:R.128 E4M.3: 20 residues within 4Å: Chain C: 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 Chain E: E.26, R.27, A.28 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain E Hydrophobic interactions: C:V.42, C:A.127, C:F.222, E:R.27, E:A.28 Hydrogen bonds: C:N.13, C:A.123, C:L.125, C:R.128, C:R.129, C:R.129, C:N.141, C:N.141, C:C.221, C:Y.230, E:R.27 Water bridges: C:G.15, C:G.15, C:R.129 Salt bridges: C:R.128 E4M.5: 20 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 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:N.141, D:N.141, D:N.141, D:C.221, A:R.27 Water bridges: D:R.128 Salt bridges: D:R.128 E4M.7: 19 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 18 PLIP interactions: 16 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.128, E:R.129, E:R.129, E:N.141, E:N.141, E:C.221, C:R.27 Water bridges: E:R.129, E:R.129 Salt bridges: E:R.128 E4M.10: 19 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 18 PLIP interactions: 16 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:V.42, F:A.127, F:F.222, B:A.28 Hydrogen bonds: F:N.13, F:G.15, F:A.123, F:L.125, F:R.128, F:R.129, F:R.129, F:N.141, F:N.141, F:C.221, B:R.27 Water bridges: F:R.129, F:R.129 Salt bridges: F:R.128

5 x CA: CALCIUM ION(Non-covalent)

CA.4: 7 residues within 4Å: Chain C: R.129, E.130, F.131, L.132, D.133 Chain E: R.263, P.265 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:R.129 CA.6: 6 residues within 4Å: Chain D: S.257, N.258 Chain E: S.257, N.258 Chain F: S.257, N.258 No protein-ligand interaction detected (PLIP) CA.8: 2 residues within 4Å: Chain E: E.85, D.89 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.85, E:D.89, E:D.89 CA.9: 7 residues within 4Å: Chain E: D.259, A.260, V.261, R.276, K.277, F.278 Chain F: Y.198 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Metal complexes: E:D.259, E:R.276, F:Y.198 CA.11: 6 residues within 4Å: Chain D: Y.198 Chain F: D.259, A.260, V.261, R.276, F.278 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: D:Y.198, F:D.259, F:R.276, H2O.21

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
G

B
H

C
I

D
J

E
K

F
L

F420-dependent methylenetetrahydromethanopterin dehydrogenase

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