SMTL ID : 2fhj.1

Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

17 x K: POTASSIUM ION(Non-covalent)

K.1: 4 residues within 4Å: Chain A: E.113, T.161, T.162, L.251 Ligand excluded by PLIP K.2: 5 residues within 4Å: Chain A: V.97, M.98, A.100, A.103, F.152 Ligand excluded by PLIP K.3: 5 residues within 4Å: Chain A: D.57, I.190, K.191, V.193, A.196 Ligand excluded by PLIP K.4: 5 residues within 4Å: Chain A: T.41, G.44, A.54, P.199 Chain B: E.39 Ligand excluded by PLIP K.9: 5 residues within 4Å: Chain A: E.39 Chain B: T.41, G.44, A.54, P.199 Ligand excluded by PLIP K.10: 5 residues within 4Å: Chain B: D.57, I.190, K.191, V.193, A.196 Ligand excluded by PLIP K.11: 5 residues within 4Å: Chain B: V.97, M.98, A.100, A.103, F.152 Ligand excluded by PLIP K.12: 5 residues within 4Å: Chain B: E.113, E.115, T.161, T.162, L.251 Ligand excluded by PLIP K.13: 2 residues within 4Å: Chain B: G.69 Chain C: E.265 Ligand excluded by PLIP K.14: 5 residues within 4Å: Chain C: D.57, I.190, K.191, V.193, A.196 Ligand excluded by PLIP K.15: 5 residues within 4Å: Chain C: V.97, M.98, A.100, A.103, F.152 Ligand excluded by PLIP K.16: 5 residues within 4Å: Chain C: T.41, G.44, A.54, P.199 Chain D: E.39 Ligand excluded by PLIP K.17: 4 residues within 4Å: Chain C: E.113, T.161, T.162, L.251 Ligand excluded by PLIP K.21: 5 residues within 4Å: Chain D: D.57, I.190, K.191, V.193, A.196 Ligand excluded by PLIP K.22: 5 residues within 4Å: Chain D: V.97, M.98, A.100, A.103, F.152 Ligand excluded by PLIP K.23: 4 residues within 4Å: Chain D: E.113, T.161, T.162, L.251 Ligand excluded by PLIP K.24: 6 residues within 4Å: Chain C: E.39 Chain D: T.41, G.44, A.54, P.199 Ligands: PE4.27 Ligand excluded by PLIP

4 x MFN: N-[4,5,7-TRICARBOXYHEPTANOYL]-L-GAMMA-GLUTAMYL-N-{2-[4-({5-[(FORMYLAMINO)METHYL]-3-FURYL}METHOXY)PHENYL]ETHYL}-D-GLUTAMINE(Non-covalent)

MFN.5: 20 residues within 4Å: Chain A: L.90, G.94, Q.95, M.98, T.99, Y.122, K.123, F.126, F.127 Chain B: S.46, I.48, F.200, V.205, S.207, A.208, S.209, F.218, L.219, A.221, E.245 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.99, A:F.126, A:F.127, A:F.127, B:I.48 Hydrogen bonds: A:Q.95, A:Y.122, A:K.123, B:S.209 Salt bridges: A:K.123 MFN.6: 19 residues within 4Å: Chain A: S.46, I.48, M.49, F.200, V.205, S.207, S.209, F.218, L.219, P.220, A.221 Chain B: G.94, Q.95, M.98, T.99, K.123, L.124, F.127 Ligands: H4Z.7 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.48, A:L.219, A:P.220, A:P.220, B:T.99, B:F.127 Hydrogen bonds: A:S.46, A:S.209, B:Q.95 MFN.18: 17 residues within 4Å: Chain C: L.90, G.94, Q.95, M.98, T.99, K.123, L.124, F.126, F.127 Chain D: M.49, Y.170, F.200, V.205, S.207, A.208, S.209, E.245 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:S.209, D:S.209, C:Q.95, C:K.123, C:F.127 Hydrophobic interactions: C:T.99, C:K.123, C:F.126, C:F.127, C:F.127 MFN.25: 19 residues within 4Å: Chain C: S.46, M.49, F.200, V.205, S.207, A.208, S.209, L.219, A.221, E.245 Chain D: G.94, Q.95, M.98, T.99, K.123, L.124, F.126, F.127 Ligands: H4Z.19 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:T.99, D:K.123, D:L.124, D:F.127, C:L.219 Hydrogen bonds: D:Q.95, D:K.123, C:S.209, C:S.209 Water bridges: D:K.123 Salt bridges: D:K.123

2 x H4Z: 5-(4-{[1-(2-AMINO-5-FORMYL-7-METHYL-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL)ETHYL]AMINO}PHENYL)-5-DEOXY-1-O-{5-O-[(1,3-DICARBOXYPROPOXY)(HYDROXY)PHOSPHORYL]PENTOFURANOSYL}PENTITOL(Non-covalent)

H4Z.7: 14 residues within 4Å: Chain A: E.14, F.16, V.47, G.166, Y.170, S.209, K.210, V.211, A.221, E.245, G.279, F.281, L.285 Ligands: MFN.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.16, A:F.16, A:V.47, A:V.211, A:A.221, A:F.281, A:L.285 Hydrogen bonds: A:Y.170, A:Y.170 Salt bridges: A:E.245 H4Z.19: 11 residues within 4Å: Chain C: I.48, N.168, Y.170, S.209, K.210, V.211, A.221, E.245, G.279, F.281 Ligands: MFN.25 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.48, C:A.221 Hydrogen bonds: C:Y.170, C:S.209 Salt bridges: C:E.245

3 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.8: 11 residues within 4Å: Chain A: P.177, L.180, Q.181, E.184 Chain B: W.32 Chain C: P.177, L.180, Q.181, E.184 Chain D: S.29, W.32 7 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Water bridges: D:S.29, D:K.31, D:K.31, B:K.31, C:A.185 Hydrogen bonds: A:E.184, C:E.184 PE4.26: 14 residues within 4Å: Chain C: K.31, W.32, M.34, I.35, K.38 Chain D: M.34, K.38, G.59, Y.60, E.184, V.187, K.191, G.202 Ligands: PE4.27 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:W.32, D:E.184 Hydrogen bonds: C:K.31, D:K.38, D:K.191 PE4.27: 14 residues within 4Å: Chain C: I.35, K.38, E.39 Chain D: K.38, T.41, G.42, G.55, I.56, V.187, K.191, A.198, G.202 Ligands: K.24, PE4.26 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.38, D:I.56, D:A.198 Hydrophobic interactions: C:I.35

1 x PE3: 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL(Non-functional Binders)

PE3.20: 4 residues within 4Å: Chain B: H.30, K.31, Y.60 Chain C: K.191 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:K.31 Hydrogen bonds: B:Y.60, B:Y.60, C:K.191 Water bridges: B:K.31, C:E.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Acharya, P. et al., The structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes. J.Mol.Biol. (2006)

Release Date

2006-03-07

Peptides

Formylmethanofuran--tetrahydromethanopterin formyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Formylmethanofuran--tetrahydromethanopterin formyltransferase

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