SMTL ID : 8axz.1

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with S-adenosylmethionine, adenosin and diphosphono-aminophosphonic acid.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-dimer

Ligands

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

PPK.1: 17 residues within 4Å: Chain A: H.32, D.34, K.184, D.261, R.267, K.268 Chain B: E.60, D.137, G.283, A.284, K.288, D.294 Ligands: MG.2, MG.3, K.4, SAM.6, ADN.7 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:D.137, B:G.282, B:A.284, B:K.288, B:K.288, B:K.288, A:R.267, A:R.267 Water bridges: A:K.184 Salt bridges: A:H.32, A:K.184, A:K.268 PPK.10: 17 residues within 4Å: Chain A: E.60, D.137, G.283, A.284, K.288, D.294 Chain B: H.32, D.34, K.184, D.261, R.267, K.268 Ligands: MG.11, MG.12, K.13, SAM.15, ADN.16 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.267, B:R.267, A:D.137, A:G.282, A:A.284, A:K.288, A:K.288, A:K.288 Water bridges: B:K.184 Salt bridges: B:H.32, B:K.184, B:K.268

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.34, K.268 Ligands: PPK.1, K.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.34, H2O.1, H2O.3 MG.3: 3 residues within 4Å: Chain A: K.268 Chain B: D.294 Ligands: PPK.1 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain B: D.34, K.268 Ligands: PPK.10, K.13 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.34, H2O.12, H2O.13 MG.12: 3 residues within 4Å: Chain A: D.294 Chain B: K.268 Ligands: PPK.10 No protein-ligand interaction detected (PLIP)

4 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: D.261, A.262 Chain B: E.60 Ligands: PPK.1, MG.2 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.60, A:D.261, A:A.262, H2O.15 K.5: 4 residues within 4Å: Chain A: M.141, F.142, H.280, G.281 No protein-ligand interaction detected (PLIP) K.13: 5 residues within 4Å: Chain A: E.60 Chain B: D.261, A.262 Ligands: PPK.10, MG.11 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.60, B:D.261, B:A.262, H2O.4 K.14: 4 residues within 4Å: Chain B: M.141, F.142, H.280, G.281 No protein-ligand interaction detected (PLIP)

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

SAM.6: 20 residues within 4Å: Chain A: H.32, P.33, D.182, K.184, S.209, S.250, R.252, F.253, D.261 Chain B: A.58, E.73, Q.116, D.119, I.120, G.136, D.137, K.292, I.325 Ligands: PPK.1, ADN.7 21 PLIP interactions: 10 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:E.73, B:E.73, B:Q.116, A:D.182, A:S.250, A:R.252, A:D.261, A:D.261 Water bridges: B:I.120, B:I.120, B:D.137, B:K.292, B:K.292, A:S.209, A:S.250, A:A.262 Salt bridges: B:D.137, B:K.292, A:D.261 pi-Stacking: A:F.253, A:F.253 SAM.15: 20 residues within 4Å: Chain A: A.58, E.73, Q.116, D.119, I.120, G.136, D.137, K.292, I.325 Chain B: H.32, P.33, D.182, K.184, S.209, S.250, R.252, F.253, D.261 Ligands: PPK.10, ADN.16 22 PLIP interactions: 12 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:D.182, B:S.250, B:R.252, B:D.261, B:D.261, B:D.261, A:E.73, A:E.73, A:Q.116 Water bridges: B:S.209, B:S.250, B:A.262, A:I.120, A:I.120, A:D.137, A:K.292, A:K.292 Salt bridges: B:D.261, A:D.137, A:K.292 pi-Stacking: B:F.253, B:F.253

2 x ADN: ADENOSINE(Non-covalent)

ADN.7: 15 residues within 4Å: Chain A: H.32, P.33, D.182, K.184, S.250, R.252, F.253, I.255, D.261 Chain B: D.119, I.120, D.137, I.325 Ligands: PPK.1, SAM.6 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.182, A:S.250, A:R.252, A:D.261 Water bridges: A:S.209, A:S.250, B:I.120, B:I.120, B:D.137 pi-Stacking: A:F.253, A:F.253 ADN.16: 15 residues within 4Å: Chain A: D.119, I.120, D.137, I.325 Chain B: H.32, P.33, D.182, K.184, S.250, R.252, F.253, I.255, D.261 Ligands: PPK.10, SAM.15 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain B Water bridges: A:I.120, A:I.120, A:D.137, B:S.209, B:S.250 Hydrogen bonds: B:D.182, B:S.250, B:R.252, B:D.261, B:D.261 pi-Stacking: B:F.253, B:F.253

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

PEG.8: 4 residues within 4Å: Chain A: K.353, K.354, N.355, F.356 No protein-ligand interaction detected (PLIP) PEG.17: 4 residues within 4Å: Chain B: K.353, K.354, N.355, F.356 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 11 residues within 4Å: Chain A: K.64, T.65, I.255, Q.259, G.260 Chain B: E.73, E.114, Q.115, Q.116, S.117, P.118 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.64, A:Q.259, A:Q.259, B:Q.115 Water bridges: A:Q.259 GOL.18: 11 residues within 4Å: Chain A: E.73, E.114, Q.115, Q.116, S.117, P.118 Chain B: K.64, T.65, I.255, Q.259, G.260 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.64, B:Q.259, B:Q.259, A:Q.115 Water bridges: B:Q.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nawrotek, A. et al., Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with S-adenosylmethionine, adenosin and diphosphono-aminophosphonic acid. To Be Published

Release Date

2022-10-05

Peptides

S-adenosylmethionine synthase isoform type-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

S-adenosylmethionine synthase isoform type-2