SMTL ID : 6fcb.1

Human Methionine Adenosyltransferase II mutant (P115G)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x PPK: (DIPHOSPHONO)AMINOPHOSPHONIC ACID(Non-covalent)

PPK.1: 16 residues within 4Å: Chain A: H.29, D.31, K.181, D.258, R.264, K.265 Chain B: D.134, G.279, G.280, A.281, K.285, D.291 Ligands: MG.2, MG.3, K.4, SAM.5 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.258, A:R.264, A:R.264, A:R.264, A:K.265, B:A.281, B:K.285, B:K.285 Salt bridges: A:H.29, A:K.181, A:K.265 PPK.7: 16 residues within 4Å: Chain A: D.134, G.279, G.280, A.281, K.285, D.291 Chain B: H.29, D.31, K.181, D.258, R.264, K.265 Ligands: MG.8, MG.9, K.10, SAM.11 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:A.281, A:K.285, A:K.285, B:D.258, B:R.264, B:R.264, B:R.264, B:K.265 Salt bridges: B:H.29, B:K.181, B:K.265 PPK.13: 16 residues within 4Å: Chain C: H.29, D.31, K.181, D.258, R.264, K.265 Chain D: D.134, G.279, G.280, A.281, K.285, D.291 Ligands: MG.14, MG.15, K.16, SAM.17 11 PLIP interactions: 3 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:A.281, D:K.285, D:K.285, C:D.258, C:R.264, C:R.264, C:R.264, C:K.265 Salt bridges: C:H.29, C:K.181, C:K.265 PPK.19: 16 residues within 4Å: Chain C: D.134, G.279, G.280, A.281, K.285, D.291 Chain D: H.29, D.31, K.181, D.258, R.264, K.265 Ligands: MG.20, MG.21, K.22, SAM.23 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:D.258, D:R.264, D:R.264, D:R.264, D:K.265, C:A.281, C:K.285, C:K.285 Salt bridges: D:H.29, D:K.181, D:K.265

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.31, A.259, R.264 Chain B: E.57 Ligands: PPK.1, K.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.31, A:D.31 MG.3: 3 residues within 4Å: Chain B: D.134, D.291 Ligands: PPK.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.291 MG.8: 6 residues within 4Å: Chain A: E.57 Chain B: D.31, A.259, R.264 Ligands: PPK.7, K.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.31, B:D.31 MG.9: 3 residues within 4Å: Chain A: D.134, D.291 Ligands: PPK.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.291 MG.14: 6 residues within 4Å: Chain C: D.31, A.259, R.264 Chain D: E.57 Ligands: PPK.13, K.16 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.31, C:D.31 MG.15: 3 residues within 4Å: Chain D: D.134, D.291 Ligands: PPK.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.291 MG.20: 6 residues within 4Å: Chain C: E.57 Chain D: D.31, A.259, R.264 Ligands: PPK.19, K.22 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.31, D:D.31 MG.21: 3 residues within 4Å: Chain C: D.134, D.291 Ligands: PPK.19 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.291

4 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: D.258, A.259 Chain B: E.57 Ligands: PPK.1, MG.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:A.259, B:E.57 K.10: 5 residues within 4Å: Chain A: E.57 Chain B: D.258, A.259 Ligands: PPK.7, MG.8 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:E.57, B:A.259 K.16: 5 residues within 4Å: Chain C: D.258, A.259 Chain D: E.57 Ligands: PPK.13, MG.14 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Metal complexes: C:A.259, D:E.57 K.22: 5 residues within 4Å: Chain C: E.57 Chain D: D.258, A.259 Ligands: PPK.19, MG.20 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Metal complexes: C:E.57, D:A.259

4 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.5: 19 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: A.55, E.70, Q.113, D.116, I.117, G.133, D.134, K.289 Ligands: PPK.1 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:E.70, B:E.70, A:D.179, A:S.247, A:R.249, A:D.258 Salt bridges: B:D.134, B:K.289, A:D.258 pi-Stacking: A:F.250, A:F.250 SAM.11: 19 residues within 4Å: Chain A: A.55, E.70, Q.113, D.116, I.117, G.133, D.134, K.289 Chain B: H.29, P.30, D.179, K.181, S.206, S.247, R.249, F.250, I.252, D.258 Ligands: PPK.7 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.179, B:S.247, B:R.249, B:D.258, A:E.70, A:E.70 Salt bridges: B:D.258, A:D.134, A:K.289 pi-Stacking: B:F.250, B:F.250 SAM.17: 19 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: A.55, E.70, Q.113, D.116, I.117, G.133, D.134, K.289 Ligands: PPK.13 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:D.179, C:S.247, C:R.249, C:D.258, C:D.258, D:E.70, D:E.70, D:E.70 Salt bridges: C:D.258, D:D.134, D:K.289 pi-Stacking: C:F.250, C:F.250 SAM.23: 19 residues within 4Å: Chain C: A.55, E.70, Q.113, D.116, I.117, G.133, D.134, K.289 Chain D: H.29, P.30, D.179, K.181, S.206, S.247, R.249, F.250, I.252, D.258 Ligands: PPK.19 13 PLIP interactions: 8 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:D.179, D:S.247, D:R.249, D:D.258, D:D.258, C:E.70, C:E.70, C:E.70 Salt bridges: D:D.258, C:D.134, C:K.289 pi-Stacking: D:F.250, D:F.250

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

PEG.6: 4 residues within 4Å: Chain A: A.40, D.43, Q.47, Q.372 No protein-ligand interaction detected (PLIP) PEG.12: 4 residues within 4Å: Chain B: A.40, D.43, Q.47, Q.372 No protein-ligand interaction detected (PLIP) PEG.18: 4 residues within 4Å: Chain C: A.40, D.43, Q.47, Q.372 No protein-ligand interaction detected (PLIP) PEG.24: 4 residues within 4Å: Chain D: A.40, D.43, Q.47, Q.372 No protein-ligand interaction detected (PLIP)

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