SMTL ID : 4qq8.1

Crystal structure of the formolase FLS in space group P 43 21 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.88 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.448, N.475, S.477, G.479 Ligands: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.448, A:S.477, H2O.1 MG.5: 5 residues within 4Å: Chain B: D.448, M.473, N.475, S.477 Ligands: TPP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.448, B:S.477 MG.7: 6 residues within 4Å: Chain C: D.448, G.449, N.475, S.477, G.479 Ligands: TPP.8 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.448, C:S.477, H2O.1 MG.10: 6 residues within 4Å: Chain D: D.448, G.449, N.475, S.477, G.479 Ligands: TPP.11 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.448, D:S.477, H2O.1

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 27 residues within 4Å: Chain A: G.393, G.394, L.395, T.396, N.419, S.420, M.421, G.447, D.448, G.449, S.450, Y.453, N.475, S.477, W.478, G.479, W.480, T.481 Chain B: H.26, G.27, E.50, T.73, G.76, G.77, N.80, Q.113 Ligands: MG.1 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.394, A:L.395, A:T.396, A:T.396, A:N.419, A:M.421, A:G.447, A:D.448, A:G.449, A:S.450, A:N.475, A:G.479, A:W.480 Water bridges: A:D.448, A:D.448 Hydrophobic interactions: B:T.73 TPP.6: 27 residues within 4Å: Chain A: H.26, G.27, E.50, T.73, G.76, G.77, N.80, Q.113 Chain B: G.393, G.394, L.395, T.396, N.419, S.420, M.421, G.447, D.448, G.449, S.450, Y.453, N.475, S.477, W.478, G.479, W.480, T.481 Ligands: MG.5 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.481, A:T.73 Hydrogen bonds: B:G.394, B:L.395, B:T.396, B:T.396, B:N.419, B:M.421, B:G.447, B:D.448, B:G.449, B:S.450, B:Y.453, B:N.475, B:G.479, B:W.480 TPP.8: 28 residues within 4Å: Chain C: G.393, G.394, L.395, T.396, N.419, S.420, M.421, G.447, D.448, G.449, S.450, Y.453, N.475, S.477, W.478, G.479, W.480, T.481 Chain D: L.25, H.26, G.27, E.50, T.73, G.76, G.77, N.80, Q.113 Ligands: MG.7 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.394, C:L.395, C:T.396, C:T.396, C:N.419, C:M.421, C:G.449, C:S.450, C:Y.453, C:N.475, C:N.475, C:G.479, C:W.480 Water bridges: C:D.448, C:D.448 Hydrophobic interactions: D:T.73 TPP.11: 28 residues within 4Å: Chain C: L.25, H.26, G.27, E.50, T.73, G.76, G.77, N.80, Q.113 Chain D: G.393, G.394, L.395, T.396, N.419, S.420, M.421, G.447, D.448, G.449, S.450, Y.453, N.475, S.477, W.478, G.479, W.480, T.481 Ligands: MG.10 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.394, D:L.395, D:T.396, D:N.419, D:M.421, D:G.447, D:D.448, D:G.449, D:S.450, D:N.475, D:N.475, D:G.479, D:W.480 Water bridges: D:T.396, D:D.448 Hydrophobic interactions: C:T.73

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 2 residues within 4Å: Chain A: K.381, H.382 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: D.514, Y.516, Q.530, H.534, R.536 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.536, A:R.536 EDO.9: 4 residues within 4Å: Chain C: R.89, A.123, T.126, K.127 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.89, C:K.127 EDO.12: 2 residues within 4Å: Chain D: K.381, H.382 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Siegel, J.B. et al., Computational protein design enables a novel one-carbon assimilation pathway. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-03-11

Peptides

Formolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Formolase