SMTL ID : 6g6r.1

Human Methionine Adenosyltransferase II with SAMe and PPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-tetramer

Ligands

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

PPK.1: 17 residues within 4Å: Chain A: H.29, D.31, K.181, D.258, R.264, K.265 Chain B: E.57, D.134, G.279, G.280, A.281, K.285, D.291 Ligands: MG.2, MG.3, K.4, SAM.6 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.258, A:R.264, A:R.264, B:A.281, B:K.285, B:K.285 Water bridges: A:K.181, A:K.181, A:K.181, B:D.291, B:D.291 Salt bridges: A:H.29, A:K.181, A:K.265 PPK.10: 17 residues within 4Å: Chain A: E.57, 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.11, MG.12, K.13, SAM.15 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.258, B:R.264, B:R.264, A:A.281, A:K.285, A:K.285 Water bridges: B:K.181, B:K.181, B:K.181, A:D.291, A:D.291 Salt bridges: B:H.29, B:K.181, B:K.265 PPK.19: 17 residues within 4Å: Chain C: H.29, D.31, K.181, D.258, R.264, K.265 Chain D: E.57, D.134, G.279, G.280, A.281, K.285, D.291 Ligands: MG.20, MG.21, K.22, SAM.24 12 PLIP interactions: 3 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:A.281, D:K.285, D:K.285, C:D.258, C:R.264, C:R.264 Water bridges: C:K.181, C:K.181, C:K.181 Salt bridges: C:H.29, C:K.181, C:K.265 PPK.28: 17 residues within 4Å: Chain C: E.57, 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.29, MG.30, K.31, SAM.33 13 PLIP interactions: 4 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:E.57, C:A.281, C:K.285, C:K.285, D:D.258, D:R.264, D:R.264 Water bridges: D:K.181, D:K.181, D:K.181 Salt bridges: D:H.29, D:K.181, D:K.265

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.31, R.264, K.265 Ligands: PPK.1, K.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.31, H2O.2, H2O.2 MG.3: 4 residues within 4Å: Chain A: E.23, K.265 Chain B: D.291 Ligands: PPK.1 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain B: D.31, R.264, K.265 Ligands: PPK.10, K.13 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.31, H2O.18, H2O.18 MG.12: 4 residues within 4Å: Chain A: D.291 Chain B: E.23, K.265 Ligands: PPK.10 No protein-ligand interaction detected (PLIP) MG.20: 5 residues within 4Å: Chain C: D.31, R.264, K.265 Ligands: PPK.19, K.22 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.31, H2O.33, H2O.34 MG.21: 4 residues within 4Å: Chain C: E.23, K.265 Chain D: D.291 Ligands: PPK.19 No protein-ligand interaction detected (PLIP) MG.29: 5 residues within 4Å: Chain D: D.31, R.264, K.265 Ligands: PPK.28, K.31 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.31, H2O.49, H2O.50 MG.30: 4 residues within 4Å: Chain C: D.291 Chain D: E.23, K.265 Ligands: PPK.28 No protein-ligand interaction detected (PLIP)

8 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 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.57, A:D.258, A:A.259 K.5: 4 residues within 4Å: Chain A: M.138, F.139, H.277, G.278 No protein-ligand interaction detected (PLIP) K.13: 5 residues within 4Å: Chain A: E.57 Chain B: D.258, A.259 Ligands: PPK.10, MG.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.258, B:A.259, A:E.57 K.14: 4 residues within 4Å: Chain B: M.138, F.139, H.277, G.278 No protein-ligand interaction detected (PLIP) K.22: 5 residues within 4Å: Chain C: D.258, A.259 Chain D: E.57 Ligands: PPK.19, MG.20 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Metal complexes: C:D.258, C:A.259, D:E.57 K.23: 4 residues within 4Å: Chain C: M.138, F.139, H.277, G.278 No protein-ligand interaction detected (PLIP) K.31: 5 residues within 4Å: Chain C: E.57 Chain D: D.258, A.259 Ligands: PPK.28, MG.29 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Metal complexes: D:D.258, D:A.259, C:E.57 K.32: 4 residues within 4Å: Chain D: M.138, F.139, H.277, G.278 No protein-ligand interaction detected (PLIP)

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

SAM.6: 19 residues within 4Å: Chain A: H.29, P.30, D.179, K.181, 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, I.322 Ligands: PPK.1 20 PLIP interactions: 12 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:D.179, A:S.247, A:R.249, A:D.258, A:D.258, A:D.258, B:E.70, B:Q.113 Water bridges: A:S.206, A:S.247, A:A.259, B:I.117, B:I.117, B:K.289, B:K.289 Salt bridges: A:D.258, B:D.134, B:K.289 pi-Stacking: A:F.250, A:F.250 SAM.15: 19 residues within 4Å: Chain A: A.55, E.70, Q.113, D.116, I.117, G.133, D.134, K.289, I.322 Chain B: H.29, P.30, D.179, K.181, S.247, R.249, F.250, I.252, D.258 Ligands: PPK.10 20 PLIP interactions: 12 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:D.179, B:S.247, B:R.249, B:D.258, B:D.258, B:D.258, A:E.70, A:Q.113 Water bridges: B:S.206, B:S.247, B:A.259, A:I.117, A:I.117, A:K.289, A:K.289 Salt bridges: B:D.258, A:D.134, A:K.289 pi-Stacking: B:F.250, B:F.250 SAM.24: 19 residues within 4Å: Chain C: H.29, P.30, D.179, K.181, 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, I.322 Ligands: PPK.19 22 PLIP interactions: 10 interactions with chain D, 12 interactions with chain C Hydrogen bonds: D:E.70, D:E.70, D:Q.113, C:D.179, C:S.247, C:R.249, C:D.258, C:D.258, C:D.258 Water bridges: D:I.117, D:I.117, D:D.134, D:K.289, D:K.289, C:S.206, C:S.247, C:A.259 Salt bridges: D:D.134, D:K.289, C:D.258 pi-Stacking: C:F.250, C:F.250 SAM.33: 19 residues within 4Å: Chain C: A.55, E.70, Q.113, D.116, I.117, G.133, D.134, K.289, I.322 Chain D: H.29, P.30, D.179, K.181, S.247, R.249, F.250, I.252, D.258 Ligands: PPK.28 22 PLIP interactions: 10 interactions with chain C, 12 interactions with chain D Hydrogen bonds: C:E.70, C:E.70, C:Q.113, D:D.179, D:S.247, D:R.249, D:D.258, D:D.258, D:D.258 Water bridges: C:I.117, C:I.117, C:D.134, C:K.289, C:K.289, D:S.206, D:S.247, D:A.259 Salt bridges: C:D.134, C:K.289, D:D.258 pi-Stacking: D:F.250, D:F.250

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

EDO.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.34: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PG4.8: 6 residues within 4Å: Chain A: Q.36, H.89, Q.372, R.373, Y.377, R.382 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.169, A:R.382 PG4.9: 9 residues within 4Å: Chain A: F.333, Y.335 Chain B: F.18, Q.190, G.193, V.195, W.274, R.313 Ligands: PG4.18 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.313 Water bridges: B:Y.335, B:Y.335, A:Y.335 PG4.17: 6 residues within 4Å: Chain B: Q.36, H.89, Q.372, R.373, Y.377, R.382 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.169, B:R.382 PG4.18: 9 residues within 4Å: Chain A: F.18, Q.190, G.193, V.195, W.274, R.313 Chain B: F.333, Y.335 Ligands: PG4.9 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:Y.335, A:Y.335, A:Y.335 Hydrogen bonds: A:R.313 PG4.26: 6 residues within 4Å: Chain C: Q.36, H.89, Q.372, R.373, Y.377, R.382 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.169, C:R.382 PG4.27: 9 residues within 4Å: Chain C: F.333, Y.335 Chain D: F.18, Q.190, G.193, V.195, W.274, R.313 Ligands: PG4.36 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.313 Water bridges: D:R.313, D:Y.335, C:Y.335 PG4.35: 6 residues within 4Å: Chain D: Q.36, H.89, Q.372, R.373, Y.377, R.382 2 PLIP interactions: 2 interactions with chain D Water bridges: D:R.169, D:R.382 PG4.36: 9 residues within 4Å: Chain C: F.18, Q.190, G.193, V.195, W.274, R.313 Chain D: F.333, Y.335 Ligands: PG4.27 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Water bridges: D:Y.335, C:R.313, C:Y.335 Hydrogen bonds: C:R.313

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

2019-04-10

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

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