SMTL ID : 1z69.1

Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-tetramer

Ligands

4 x F42: COENZYME F420(Non-covalent)

F42.1: 23 residues within 4Å: Chain A: T.34, D.35, H.36, G.61, V.62, P.94, G.95, D.96, W.107, K.109, P.110, L.111, A.112, G.156, A.157, Q.158, G.159, P.160, K.161, M.162, L.174, N.176, Y.209 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:V.62, A:W.107, A:K.109, A:P.110, A:L.111, A:L.111, A:K.161, A:Y.209 Hydrogen bonds: A:D.35, A:D.35, A:V.62, A:G.95, A:G.95, A:D.96, A:A.112, A:A.157, A:Q.158, A:Q.158, A:G.159, A:K.161, A:M.162, A:L.174, A:N.176 Water bridges: A:N.64, A:N.64 F42.3: 22 residues within 4Å: Chain B: T.34, D.35, H.36, G.61, V.62, P.94, G.95, D.96, W.107, K.109, P.110, L.111, G.156, A.157, Q.158, G.159, P.160, K.161, M.162, L.174, N.176, Y.209 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:W.107, B:K.109, B:P.110, B:L.111, B:Y.209, B:Y.209 Hydrogen bonds: B:D.35, B:D.35, B:V.62, B:G.95, B:G.95, B:D.96, B:D.96, B:A.157, B:Q.158, B:G.159, B:K.161, B:M.162, B:L.174, B:N.176 Salt bridges: B:K.109 F42.4: 23 residues within 4Å: Chain C: T.34, D.35, H.36, G.61, V.62, P.94, G.95, D.96, W.107, K.109, P.110, L.111, A.112, G.156, A.157, Q.158, G.159, P.160, K.161, M.162, L.174, N.176, Y.209 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:P.94, C:W.107, C:P.110, C:L.111, C:Y.209, C:Y.209 Hydrogen bonds: C:D.35, C:D.35, C:V.62, C:G.95, C:G.95, C:D.96, C:D.96, C:L.111, C:A.112, C:A.157, C:Q.158, C:Q.158, C:G.159, C:K.161, C:M.162, C:L.174, C:N.176 Water bridges: C:N.64 F42.6: 23 residues within 4Å: Chain D: T.34, D.35, H.36, G.61, V.62, P.94, G.95, D.96, W.107, K.109, P.110, L.111, A.112, G.156, A.157, Q.158, G.159, P.160, K.161, M.162, L.174, N.176, Y.209 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:P.94, D:W.107, D:K.109, D:P.110, D:L.111, D:Y.209, D:Y.209 Hydrogen bonds: D:D.35, D:D.35, D:V.62, D:G.95, D:G.95, D:D.96, D:L.111, D:A.112, D:A.157, D:Q.158, D:G.159, D:K.161, D:M.162, D:L.174, D:N.176 Water bridges: D:N.64, D:N.64, D:N.64, D:K.161

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 8 residues within 4Å: Chain B: A.50, L.51, T.53, N.54 Chain C: A.50, L.51, T.53, N.54 Ligand excluded by PLIP CL.5: 8 residues within 4Å: Chain A: A.50, L.51, T.53, N.54 Chain D: A.50, L.51, T.53, N.54 Ligand excluded by PLIP

1 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)

1PG.7: 9 residues within 4Å: Chain C: A.145 Chain D: V.8, S.10, H.36, N.38, N.39, V.228, F.231, S.307 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aufhammer, S.W. et al., Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420: Architecture of the F420/FMN binding site of enzymes within the nonprolyl cis-peptide containing bacterial luciferase family. Protein Sci. (2005)

Release Date

2005-06-21

Peptides

Coenzyme F420-dependent N(5),N(10)-methylenetetrahydromethanopterin reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Coenzyme F420-dependent N(5),N(10)-methylenetetrahydromethanopterin reductase