SMTL ID : 6fbo.1

Human Methionine Adenosyltransferase II mutant (S114A) in I222 crystal form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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: E.57, D.134, G.280, A.281, K.285, D.291 Ligands: MG.2, MG.3, K.4, ADN.6 15 PLIP interactions: 7 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:A.281, B:K.285, B:K.285, A:D.258, A:R.264, A:R.264, A:K.265 Water bridges: B:D.134, B:D.134, B:D.134, B:D.291, A:K.181 Salt bridges: A:H.29, A:K.181, A:K.265 PPK.14: 16 residues within 4Å: Chain A: E.57, D.134, G.280, A.281, K.285, D.291 Chain B: H.29, D.31, K.181, D.258, R.264, K.265 Ligands: MG.15, MG.16, K.17, ADN.19 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:D.258, B:R.264, B:R.264, B:K.265, A:A.281, A:K.285, A:K.285 Water bridges: B:K.181, A:D.134, A:D.134, A:D.134, A:D.291 Salt bridges: B:H.29, B:K.181, B:K.265 PPK.27: 16 residues within 4Å: Chain C: H.29, D.31, K.181, D.258, R.264, K.265 Chain D: E.57, D.134, G.280, A.281, K.285, D.291 Ligands: MG.28, MG.29, K.30, ADN.32 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:D.258, C:R.264, C:R.264, C:K.265, D:A.281, D:K.285, D:K.285 Water bridges: C:K.181 Salt bridges: C:H.29, C:K.181, C:K.265 PPK.40: 16 residues within 4Å: Chain C: E.57, D.134, G.280, A.281, K.285, D.291 Chain D: H.29, D.31, K.181, D.258, R.264, K.265 Ligands: MG.41, MG.42, K.43, ADN.45 13 PLIP interactions: 5 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:E.57, C:E.57, C:A.281, C:K.285, 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

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.31, 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.1, H2O.1 MG.3: 3 residues within 4Å: Chain A: K.265 Chain B: D.291 Ligands: PPK.1 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain B: D.31, K.265 Ligands: PPK.14, K.17 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.31, H2O.9, H2O.9 MG.16: 3 residues within 4Å: Chain A: D.291 Chain B: K.265 Ligands: PPK.14 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain C: D.31, K.265 Ligands: PPK.27, K.30 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.31, H2O.17, H2O.18 MG.29: 3 residues within 4Å: Chain C: K.265 Chain D: D.291 Ligands: PPK.27 No protein-ligand interaction detected (PLIP) MG.41: 4 residues within 4Å: Chain D: D.31, K.265 Ligands: PPK.40, K.43 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.31, H2O.26, H2O.26 MG.42: 3 residues within 4Å: Chain C: D.291 Chain D: K.265 Ligands: PPK.40 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 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.57, A:D.258, A:A.259, H2O.1, H2O.10 K.5: 4 residues within 4Å: Chain A: M.138, F.139, H.277, G.278 No protein-ligand interaction detected (PLIP) K.17: 5 residues within 4Å: Chain A: E.57 Chain B: D.258, A.259 Ligands: PPK.14, MG.15 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.1, H2O.9 K.18: 4 residues within 4Å: Chain B: M.138, F.139, H.277, G.278 No protein-ligand interaction detected (PLIP) K.30: 5 residues within 4Å: Chain C: D.258, A.259 Chain D: E.57 Ligands: PPK.27, MG.28 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:E.57, C:D.258, C:A.259, H2O.17, H2O.27 K.31: 4 residues within 4Å: Chain C: M.138, F.139, H.277, G.278 No protein-ligand interaction detected (PLIP) K.43: 5 residues within 4Å: Chain C: E.57 Chain D: D.258, A.259 Ligands: PPK.40, MG.41 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:D.258, D:A.259, C:E.57, H2O.18, H2O.26 K.44: 4 residues within 4Å: Chain D: M.138, F.139, H.277, G.278 No protein-ligand interaction detected (PLIP)

4 x ADN: ADENOSINE(Non-covalent)

ADN.6: 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: PPK.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.179, A:S.247, A:R.249, A:D.258 Water bridges: A:S.206, A:S.247 pi-Stacking: A:F.250, A:F.250 ADN.19: 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.14 8 PLIP interactions: 8 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 pi-Stacking: B:F.250, B:F.250 ADN.32: 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: PPK.27 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.179, C:S.247, C:R.249, C:D.258, C:D.258 Water bridges: C:S.206, C:S.247, D:D.116, D:D.134 pi-Stacking: C:F.250, C:F.250 ADN.45: 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.40 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.179, D:S.247, D:R.249, D:D.258, D:D.258 Water bridges: D:S.206, D:S.247, C:D.116, C:D.134 pi-Stacking: D:F.250, D:F.250

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

PG4.7: 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: PG4.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.313, B:R.313 PG4.20: 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: PG4.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.313, A:R.313 PG4.33: 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: PG4.46 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.313, D:R.313 PG4.46: 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: PG4.33 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.313, C:R.313

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

PEG.8: 6 residues within 4Å: Chain A: Q.36, H.89, Q.372, R.373, A.376, Y.377 No protein-ligand interaction detected (PLIP) PEG.9: 4 residues within 4Å: Chain A: H.158, K.159, A.162, R.382 No protein-ligand interaction detected (PLIP) PEG.21: 6 residues within 4Å: Chain B: Q.36, H.89, Q.372, R.373, A.376, Y.377 No protein-ligand interaction detected (PLIP) PEG.22: 4 residues within 4Å: Chain B: H.158, K.159, A.162, R.382 No protein-ligand interaction detected (PLIP) PEG.34: 6 residues within 4Å: Chain C: Q.36, H.89, Q.372, R.373, A.376, Y.377 No protein-ligand interaction detected (PLIP) PEG.35: 4 residues within 4Å: Chain C: H.158, K.159, A.162, R.382 No protein-ligand interaction detected (PLIP) PEG.47: 6 residues within 4Å: Chain D: Q.36, H.89, Q.372, R.373, A.376, Y.377 No protein-ligand interaction detected (PLIP) PEG.48: 4 residues within 4Å: Chain D: H.158, K.159, A.162, R.382 No protein-ligand interaction detected (PLIP)

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

EDO.10: 4 residues within 4Å: Chain A: P.327, L.328, I.330, K.350 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: R.84, K.102 Chain C: T.62, Q.256 Chain D: E.111 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: T.72, S.73, R.74 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: Q.47, Q.48, P.50 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: P.327, L.328, I.330, K.350 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: R.84, K.102 Chain C: E.111 Chain D: T.62, Q.256 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: T.72, S.73, R.74 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: Q.47, Q.48, P.50 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain C: P.327, L.328, I.330, K.350 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain A: T.62, Q.256 Chain B: E.111 Chain C: R.84, K.102 Ligand excluded by PLIP EDO.38: 3 residues within 4Å: Chain C: T.72, S.73, R.74 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain C: Q.47, Q.48, P.50 Ligand excluded by PLIP EDO.49: 4 residues within 4Å: Chain D: P.327, L.328, I.330, K.350 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain A: E.111 Chain B: T.62, Q.256 Chain D: R.84, K.102 Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain D: T.72, S.73, R.74 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain D: Q.47, Q.48, P.50 Ligand excluded by 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

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