SMTL ID : 6fbp.1

Human Methionine Adenosyltransferase II mutant (S114A) in P22121 crystal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

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

PG4.1: 11 residues within 4Å: Chain A: F.18, F.20, Q.190, G.273, W.274, G.275, R.313 Chain B: A.276, Q.317, F.333 Ligands: PG4.10 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.275, A:G.275 Water bridges: A:R.313, A:R.313, A:Y.335, B:G.275, B:Y.335 PG4.10: 10 residues within 4Å: Chain A: F.333, Y.335 Chain B: F.18, Q.190, G.193, V.195, W.274, R.313, Y.335 Ligands: PG4.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.313 Water bridges: B:Q.190, B:Y.335 PG4.13: 11 residues within 4Å: Chain C: F.18, F.20, Q.190, G.273, W.274, G.275, R.313 Chain D: A.276, Q.317, F.333 Ligands: PG4.22 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Water bridges: D:G.275, D:Y.335, C:R.313, C:R.313 Hydrogen bonds: C:G.275, C:G.275 PG4.22: 10 residues within 4Å: Chain C: F.333, Y.335 Chain D: F.18, Q.190, G.193, V.195, W.274, R.313, Y.335 Ligands: PG4.13 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.313 Water bridges: D:Q.190

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: T.146, E.148, V.155, K.159, P.232 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.232 Water bridges: A:E.147 Salt bridges: A:K.159 ACT.14: 5 residues within 4Å: Chain C: T.146, E.148, V.155, K.159, P.232 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.232 Water bridges: C:E.147 Salt bridges: C:K.159

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

EDO.3: 4 residues within 4Å: Chain A: K.228, A.229, V.230, P.232 No protein-ligand interaction detected (PLIP) EDO.6: 2 residues within 4Å: Chain A: Q.48, P.50 No protein-ligand interaction detected (PLIP) EDO.7: 1 residues within 4Å: Chain A: G.16 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.190, A:Q.190 EDO.15: 4 residues within 4Å: Chain C: K.228, A.229, V.230, P.232 No protein-ligand interaction detected (PLIP) EDO.18: 2 residues within 4Å: Chain C: Q.48, P.50 No protein-ligand interaction detected (PLIP) EDO.19: 1 residues within 4Å: Chain C: G.16 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Q.190, C:Q.190

4 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.12: 5 residues within 4Å: Chain A: E.57 Chain B: D.258, A.259 Ligands: PPK.8, MG.9 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.258, B:A.259, A:E.57, H2O.3 K.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.24: 5 residues within 4Å: Chain C: E.57 Chain D: D.258, A.259 Ligands: PPK.20, MG.21 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:E.57, D:D.258, D:A.259, H2O.21

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.291 Chain B: K.265 Ligands: PPK.8 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.291, H2O.1, H2O.2 MG.9: 5 residues within 4Å: Chain B: D.31, R.264, K.265 Ligands: PPK.8, K.12 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.31, H2O.11, H2O.12 MG.17: 3 residues within 4Å: Chain C: D.291 Chain D: K.265 Ligands: PPK.20 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.291, H2O.19, H2O.21 MG.21: 5 residues within 4Å: Chain D: D.31, R.264, K.265 Ligands: PPK.20, K.24 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.31, H2O.30, H2O.30

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

PPK.8: 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.5, MG.9, ADN.11, K.12 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.258, B:R.264, B:R.264, B:K.265, A:A.281, A:K.285 Water bridges: B:K.181, A:D.291, A:D.291 Salt bridges: B:H.29, B:K.181, B:K.265 PPK.20: 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.17, MG.21, ADN.23, K.24 11 PLIP interactions: 3 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:D.134, C:A.281, C:K.285, D:D.258, D:R.264, D:R.264, D:K.265 Water bridges: D:K.181 Salt bridges: D:H.29, D:K.181, D:K.265

2 x ADN: ADENOSINE(Non-covalent)

ADN.11: 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: PPK.8 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.179, B:S.247, B:R.249, B:D.258 Water bridges: B:S.206, B:S.247, B:G.248, B:D.258, B:D.258 pi-Stacking: B:F.250, B:F.250 ADN.23: 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: PPK.20 12 PLIP interactions: 1 interactions with chain C, 11 interactions with chain D Water bridges: C:D.116, D:S.206, D:S.247, D:G.248, D:D.258 Hydrogen bonds: D:D.179, D:S.247, D:R.249, D:D.258, D:D.258 pi-Stacking: D:F.250, D:F.250

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
B

C
A

D
B

S-adenosylmethionine synthase isoform type-2

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