SMTL ID : 1o92.1

Methionine Adenosyltransferase complexed with ADP and a L-methionine analogue

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.19 Å

Oligo State

homo-tetramer

Ligands

2 x AMB: L-2-AMINO-4-METHOXY-CIS-BUT-3-ENOIC ACID(Non-covalent)

AMB.1: 7 residues within 4Å: Chain A: D.180, S.248, R.250, F.251 Ligands: PO4.2, MG.5, ADP.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.251 AMB.11: 7 residues within 4Å: Chain C: D.180, S.248, R.250, F.251 Ligands: PO4.12, MG.15, ADP.17 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.251

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

PO4.2: 7 residues within 4Å: Chain A: E.24, H.30, K.182, K.266 Ligands: AMB.1, MG.6, PO4.8 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.30, A:K.182, A:K.266 PO4.3: 8 residues within 4Å: Chain A: K.182, Q.184, V.205, S.207, P.247, S.248 Chain B: D.135 Ligands: MG.4 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.207, 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.10 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.280, B:A.282 Salt bridges: B:K.286, A:K.266 PO4.12: 7 residues within 4Å: Chain C: E.24, H.30, K.182, K.266 Ligands: AMB.11, MG.16, PO4.18 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.24 Salt bridges: C:H.30, C:K.182, C:K.266 PO4.13: 8 residues within 4Å: Chain C: K.182, Q.184, V.205, S.207, P.247, S.248 Chain D: D.135 Ligands: MG.14 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.207, C:S.207, C:S.207 Salt bridges: C:K.182 PO4.18: 8 residues within 4Å: Chain C: R.265, K.266 Chain D: G.280, G.281, A.282, K.286 Ligands: PO4.12, K.20 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Salt bridges: C:K.266, D:K.286 Hydrogen bonds: D:G.280, D:A.282

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: S.248 Chain B: D.135, I.323 Ligands: PO4.3 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: P.31, D.180, G.255 Ligands: AMB.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.180, AMB.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.14: 4 residues within 4Å: Chain C: S.248 Chain D: D.135, I.323 Ligands: PO4.13 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain C: P.31, D.180, G.255 Ligands: AMB.11 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.180, AMB.11 MG.16: 3 residues within 4Å: Chain C: E.24, K.266 Ligands: PO4.12 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.24

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.7: 10 residues within 4Å: Chain A: Q.257, G.258, D.259 Chain B: A.56, E.71, D.135, K.286, K.290, D.292 Ligands: AMB.1 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:Q.257, A:Q.257, A:D.259, A:D.259, B:E.71, B:K.286, B:K.290, B:D.292, B:D.292 Water bridges: B:E.71 pi-Cation interactions: B:K.290 ADP.17: 10 residues within 4Å: Chain C: Q.257, G.258, D.259 Chain D: A.56, E.71, D.135, K.286, K.290, D.292 Ligands: AMB.11 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:E.71, D:E.71, D:K.286, D:K.290, D:D.292, C:Q.257, C:Q.257, C:D.259 Water bridges: D:E.71 pi-Cation interactions: D:K.290

4 x K: POTASSIUM ION(Non-covalent)

K.9: 3 residues within 4Å: Chain A: G.264, I.267 Chain B: R.265 No protein-ligand interaction detected (PLIP) K.10: 5 residues within 4Å: Chain B: G.264, A.282, S.284, K.286 Ligands: PO4.8 No protein-ligand interaction detected (PLIP) K.19: 3 residues within 4Å: Chain C: G.264, I.267 Chain D: R.265 No protein-ligand interaction detected (PLIP) K.20: 5 residues within 4Å: Chain D: G.264, A.282, S.284, K.286 Ligands: PO4.18 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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