SMTL ID : 1o9t.1

Methionine adenosyltransferase complexed with both substrates ATP and methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

2 x MET: METHIONINE(Non-covalent)

MET.1: 7 residues within 4Å: Chain A: D.180, S.248, R.250, F.251 Ligands: MG.3, MG.4, ATP.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.251 MET.10: 7 residues within 4Å: Chain C: D.180, S.248, R.250, F.251 Ligands: MG.12, MG.13, ATP.16 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.251

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 9 residues within 4Å: Chain A: K.182, V.205, S.207, P.247, S.248 Chain B: D.135, Q.136, I.323 Ligands: ATP.7 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.207, A:S.207, B:D.135, B:Q.136 Salt bridges: A:K.182 PO4.8: 9 residues within 4Å: Chain A: R.265, K.266 Chain B: G.280, G.281, A.282, K.286 Ligands: MG.5, ATP.7, K.9 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.266, B:K.286 Hydrogen bonds: B:A.282 PO4.11: 9 residues within 4Å: Chain C: K.182, V.205, S.207, P.247, S.248 Chain D: D.135, Q.136, I.323 Ligands: ATP.16 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.207, C:S.207, D:Q.136 Salt bridges: C:K.182 PO4.17: 9 residues within 4Å: Chain C: R.265, K.266 Chain D: G.280, G.281, A.282, K.286 Ligands: MG.14, ATP.16, K.18 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:A.282 Salt bridges: D:K.286, C:K.266

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: S.248 Ligands: MET.1 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain A: H.30, P.31, D.180 Ligands: MET.1, ATP.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.30, MET.1 MG.5: 4 residues within 4Å: Chain A: E.24, K.266 Ligands: ATP.7, PO4.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.24 MG.12: 2 residues within 4Å: Chain C: S.248 Ligands: MET.10 No protein-ligand interaction detected (PLIP) MG.13: 5 residues within 4Å: Chain C: H.30, P.31, D.180 Ligands: MET.10, ATP.16 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain C Metal complexes: MET.10, C:H.30 MG.14: 4 residues within 4Å: Chain C: E.24, K.266 Ligands: ATP.16, PO4.17 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.24

4 x K: POTASSIUM ION(Non-covalent)

K.6: 3 residues within 4Å: Chain A: G.264, I.267 Chain B: R.265 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.264 K.9: 4 residues within 4Å: Chain B: A.282, S.284, K.286 Ligands: PO4.8 No protein-ligand interaction detected (PLIP) K.15: 3 residues within 4Å: Chain C: G.264, I.267 Chain D: R.265 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:G.264 K.18: 4 residues within 4Å: Chain D: A.282, S.284, K.286 Ligands: PO4.17 No protein-ligand interaction detected (PLIP)

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.7: 13 residues within 4Å: Chain A: H.30, K.182, K.266 Chain B: A.56, E.71, D.135, K.286, K.290 Ligands: MET.1, PO4.2, MG.4, MG.5, PO4.8 10 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B, 1 Ligand-Ligand interactions Salt bridges: A:H.30, A:K.182, A:K.182, A:K.182, A:K.266 Hydrogen bonds: B:E.71, B:K.286, B:K.286, B:K.290, M.1 ATP.16: 13 residues within 4Å: Chain C: H.30, K.182, K.266 Chain D: A.56, E.71, D.135, K.286, K.290 Ligands: MET.10, PO4.11, MG.13, MG.14, PO4.17 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:E.71, D:E.71, D:K.286, D:K.286, D:K.290 Salt bridges: C:H.30, C:K.182, C:K.182, C:K.182, C:K.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gonzalez, B. et al., Crystal Structures of Methionine Adenosyltransferase Complexed with Substrates and Products Reveal the Methionine-ATP Recognition and Give Insights Into the Catalytic Mechanism. J.Mol.Biol. (2003)

Release Date

2003-08-07

Peptides

S-ADENOSYLMETHIONINE SYNTHETASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

S-ADENOSYLMETHIONINE SYNTHETASE

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