SMTL ID : 1o90.1

Methionine Adenosyltransferase complexed with a L-methionine analogue

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-tetramer

Ligands

2 x LIS: (2S,4S)-2-AMINO-4,5-EPOXIPENTANOIC ACID(Non-covalent)

LIS.1: 4 residues within 4Å: Chain A: S.207, R.250, F.251 Ligands: MG.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.251 LIS.10: 4 residues within 4Å: Chain C: S.207, R.250, F.251 Ligands: MG.14 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.251

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

PO4.2: 5 residues within 4Å: Chain A: H.30, K.182, K.266 Ligands: MG.6, PO4.8 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.182 Salt bridges: A:H.30, A:K.182, A:K.266 PO4.3: 8 residues within 4Å: Chain A: K.182, V.205, S.207, P.247, S.248 Chain B: D.135, I.323 Ligands: MG.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.207, A:S.207, B:D.135 Salt bridges: A:K.182 PO4.8: 8 residues within 4Å: Chain A: R.265, K.266 Chain B: G.280, G.281, A.282, K.286 Ligands: PO4.2, K.9 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.280, B:A.282 Salt bridges: B:K.286, A:R.265, A:K.266 PO4.11: 5 residues within 4Å: Chain C: H.30, K.182, K.266 Ligands: MG.15, PO4.17 4 PLIP interactions: 4 interactions with chain C Water bridges: C:K.182 Salt bridges: C:H.30, C:K.182, C:K.266 PO4.12: 8 residues within 4Å: Chain C: K.182, V.205, S.207, P.247, S.248 Chain D: D.135, I.323 Ligands: MG.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.207, C:S.207 Salt bridges: C:K.182 PO4.17: 8 residues within 4Å: Chain C: R.265, K.266 Chain D: G.280, G.281, A.282, K.286 Ligands: PO4.11, K.18 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.280, D:A.282 Salt bridges: D:K.286, C:R.265, C:K.266

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: P.247, S.248 Chain B: D.135, I.323 Ligands: PO4.3 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: D.180 Ligands: LIS.1 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: LIS.1 MG.6: 3 residues within 4Å: Chain A: E.24, K.266 Ligands: PO4.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.24 MG.13: 5 residues within 4Å: Chain C: P.247, S.248 Chain D: D.135, I.323 Ligands: PO4.12 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain C: D.180 Ligands: LIS.10 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: LIS.10 MG.15: 3 residues within 4Å: Chain C: E.24, K.266 Ligands: PO4.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.24

4 x K: POTASSIUM ION(Non-covalent)

K.7: 3 residues within 4Å: Chain A: G.264, I.267 Chain B: R.265 No protein-ligand interaction detected (PLIP) K.9: 4 residues within 4Å: Chain B: A.282, S.284, K.286 Ligands: PO4.8 No protein-ligand interaction detected (PLIP) K.16: 3 residues within 4Å: Chain C: G.264, I.267 Chain D: R.265 No protein-ligand interaction detected (PLIP) K.18: 4 residues within 4Å: Chain D: A.282, S.284, K.286 Ligands: PO4.17 No protein-ligand interaction detected (PLIP)

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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