SMTL ID : 6fcd.1

Human Methionine Adenosyltransferase II mutant (R264A)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.23 Chain B: D.291 Ligands: PPV.6 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain A: D.31, K.265 Ligands: K.3, PPV.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.31, H2O.2, H2O.2, H2O.6 MG.11: 3 residues within 4Å: Chain A: D.291 Chain B: E.23 Ligands: PPV.16 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain B: D.31, K.265 Ligands: K.13, PPV.16 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.31, H2O.12, H2O.12, H2O.17 MG.21: 3 residues within 4Å: Chain C: E.23 Chain D: D.291 Ligands: PPV.26 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain C: D.31, K.265 Ligands: K.23, PPV.26 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.31, H2O.23, H2O.23, H2O.28 MG.31: 3 residues within 4Å: Chain C: D.291 Chain D: E.23 Ligands: PPV.36 No protein-ligand interaction detected (PLIP) MG.32: 4 residues within 4Å: Chain D: D.31, K.265 Ligands: K.33, PPV.36 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.31, H2O.33, H2O.34, H2O.38

4 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: D.258, A.259 Chain B: E.57 Ligands: MG.2, PPV.6 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.258, A:A.259, B:E.57, H2O.2, H2O.17 K.13: 5 residues within 4Å: Chain A: E.57 Chain B: D.258, A.259 Ligands: MG.12, PPV.16 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.57, B:D.258, B:A.259, H2O.6, H2O.12 K.23: 5 residues within 4Å: Chain C: D.258, A.259 Chain D: E.57 Ligands: MG.22, PPV.26 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:D.258, C:A.259, D:E.57, H2O.23, H2O.38 K.33: 5 residues within 4Å: Chain C: E.57 Chain D: D.258, A.259 Ligands: MG.32, PPV.36 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:E.57, D:D.258, D:A.259, H2O.28, H2O.33

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 8 residues within 4Å: Chain A: F.333, Y.335 Chain B: Q.190, G.193, W.274, R.313, Y.335 Ligands: PG4.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.313, B:R.313, B:Y.335 PG4.14: 8 residues within 4Å: Chain A: Q.190, G.193, W.274, R.313, Y.335 Chain B: F.333, Y.335 Ligands: PG4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.313, A:R.313, A:Y.335 PG4.24: 8 residues within 4Å: Chain C: F.333, Y.335 Chain D: Q.190, G.193, W.274, R.313, Y.335 Ligands: PG4.34 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.313, D:R.313, D:Y.335 PG4.34: 8 residues within 4Å: Chain C: Q.190, G.193, W.274, R.313, Y.335 Chain D: F.333, Y.335 Ligands: PG4.24 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.313, C:R.313, C:Y.335

4 x ADN: ADENOSINE(Non-covalent)

ADN.5: 15 residues within 4Å: Chain A: H.29, P.30, D.179, K.181, S.206, S.247, R.249, F.250, I.252, D.258 Chain B: D.116, I.117, D.134, I.322 Ligands: PPV.6 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.179, A:S.247, A:R.249, A:D.258 Water bridges: A:S.206, A:S.247, B:I.117, B:I.117 pi-Stacking: A:F.250, A:F.250 ADN.15: 15 residues within 4Å: Chain A: D.116, I.117, D.134, I.322 Chain B: H.29, P.30, D.179, K.181, S.206, S.247, R.249, F.250, I.252, D.258 Ligands: PPV.16 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B Water bridges: A:I.117, A:I.117, B:S.206, B:S.247 Hydrogen bonds: B:D.179, B:S.247, B:R.249, B:D.258 pi-Stacking: B:F.250, B:F.250 ADN.25: 15 residues within 4Å: Chain C: H.29, P.30, D.179, K.181, S.206, S.247, R.249, F.250, I.252, D.258 Chain D: D.116, I.117, D.134, I.322 Ligands: PPV.26 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.179, C:S.247, C:R.249, C:D.258 Water bridges: C:S.206, C:S.247, D:I.117, D:I.117 pi-Stacking: C:F.250, C:F.250 ADN.35: 15 residues within 4Å: Chain C: D.116, I.117, D.134, I.322 Chain D: H.29, P.30, D.179, K.181, S.206, S.247, R.249, F.250, I.252, D.258 Ligands: PPV.36 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.179, D:S.247, D:R.249, D:D.258 Water bridges: D:S.206, D:S.247, C:I.117, C:I.117 pi-Stacking: D:F.250, D:F.250

4 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.6: 12 residues within 4Å: Chain A: H.29, D.31, K.181, D.258, K.265 Chain B: D.134, K.285, D.291 Ligands: MG.1, MG.2, K.3, ADN.5 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:D.134, B:D.291 Water bridges: B:K.285, B:K.285, B:K.285, B:K.285, B:K.285, A:D.31, A:K.181, A:D.258 Salt bridges: B:K.285, A:H.29, A:K.181, A:K.265, A:K.265 PPV.16: 12 residues within 4Å: Chain A: D.134, K.285, D.291 Chain B: H.29, D.31, K.181, D.258, K.265 Ligands: MG.11, MG.12, K.13, ADN.15 15 PLIP interactions: 7 interactions with chain B, 8 interactions with chain A Water bridges: B:D.31, B:K.181, B:D.258, A:K.285, A:K.285, A:K.285, A:K.285, A:K.285 Salt bridges: B:H.29, B:K.181, B:K.265, B:K.265, A:K.285 Hydrogen bonds: A:D.134, A:D.291 PPV.26: 12 residues within 4Å: Chain C: H.29, D.31, K.181, D.258, K.265 Chain D: D.134, K.285, D.291 Ligands: MG.21, MG.22, K.23, ADN.25 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain D Water bridges: C:D.31, C:K.181, C:D.258, D:K.285, D:K.285, D:K.285, D:K.285, D:K.285 Salt bridges: C:H.29, C:K.181, C:K.265, C:K.265, D:K.285 PPV.36: 12 residues within 4Å: Chain C: D.134, K.285, D.291 Chain D: H.29, D.31, K.181, D.258, K.265 Ligands: MG.31, MG.32, K.33, ADN.35 13 PLIP interactions: 7 interactions with chain D, 6 interactions with chain C Water bridges: D:D.31, D:K.181, D:D.258, C:K.285, C:K.285, C:K.285, C:K.285, C:K.285 Salt bridges: D:H.29, D:K.181, D:K.265, D:K.265, C:K.285

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 4 residues within 4Å: Chain A: H.89, Q.372, R.373, Y.377 No protein-ligand interaction detected (PLIP) PEG.8: 3 residues within 4Å: Chain A: A.76 Chain D: R.74, A.75 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.78 PEG.17: 4 residues within 4Å: Chain B: H.89, Q.372, R.373, Y.377 No protein-ligand interaction detected (PLIP) PEG.18: 3 residues within 4Å: Chain B: A.76 Chain C: R.74, A.75 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.78 PEG.27: 4 residues within 4Å: Chain C: H.89, Q.372, R.373, Y.377 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.89 PEG.28: 3 residues within 4Å: Chain B: R.74, A.75 Chain C: A.76 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.78 PEG.37: 4 residues within 4Å: Chain D: H.89, Q.372, R.373, Y.377 1 PLIP interactions: 1 interactions with chain D Water bridges: D:H.89 PEG.38: 3 residues within 4Å: Chain A: R.74, A.75 Chain D: A.76 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.78

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

EDO.9: 6 residues within 4Å: Chain A: D.49, D.51, K.53, T.72, S.73, R.74 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.53, A:K.53, A:R.74, A:R.74 EDO.10: 6 residues within 4Å: Chain A: T.72, Q.112, Q.113, P.115, A.118, L.123 No protein-ligand interaction detected (PLIP) EDO.19: 6 residues within 4Å: Chain B: D.49, D.51, K.53, T.72, S.73, R.74 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.53, B:K.53, B:R.74, B:R.74 EDO.20: 6 residues within 4Å: Chain B: T.72, Q.112, Q.113, P.115, A.118, L.123 No protein-ligand interaction detected (PLIP) EDO.29: 6 residues within 4Å: Chain C: D.49, D.51, K.53, T.72, S.73, R.74 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.53, C:K.53, C:R.74, C:R.74 EDO.30: 6 residues within 4Å: Chain C: T.72, Q.112, Q.113, P.115, A.118, L.123 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.72 EDO.39: 6 residues within 4Å: Chain D: D.49, D.51, K.53, T.72, S.73, R.74 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.53, D:K.53, D:R.74, D:R.74 EDO.40: 6 residues within 4Å: Chain D: T.72, Q.112, Q.113, P.115, A.118, L.123 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Panmanee, J. et al., Control and regulation of S-Adenosylmethionine biosynthesis by the regulatory beta subunit and quinolone-based compounds. Febs J. (2019)

Release Date

2019-01-30

Peptides

S-adenosylmethionine synthase isoform type-2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

S-adenosylmethionine synthase isoform type-2