SMTL ID : 5a1i.1

The structure of Human MAT2A in complex with SAM, Adenosine, Methionine and PPNP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.09 Å

Oligo State

homo-tetramer

Ligands

4 x MET: METHIONINE(Non-covalent)

MET.1: 11 residues within 4Å: Chain A: D.258 Chain D: A.55, E.70, Q.113, I.117, K.285, K.289 Ligands: PPK.2, K.5, SAM.7, ADN.8 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain D Water bridges: A:A.259, D:K.289, D:K.289, D:K.289 Hydrogen bonds: D:E.70, D:Q.113 Salt bridges: D:K.289 MET.12: 11 residues within 4Å: Chain B: D.258 Chain C: A.55, E.70, Q.113, I.117, K.285, K.289 Ligands: PPK.13, K.16, SAM.18, ADN.19 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:E.70, C:E.70, C:Q.113 Water bridges: C:K.289, C:K.289, C:K.289, B:A.259 Salt bridges: C:K.289 MET.23: 11 residues within 4Å: Chain B: A.55, E.70, Q.113, I.117, K.285, K.289 Chain C: D.258 Ligands: PPK.24, K.27, SAM.29, ADN.30 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.70, B:E.70, B:Q.113 Water bridges: B:K.289, B:K.289, B:K.289, C:A.259 Salt bridges: B:K.289 MET.34: 11 residues within 4Å: Chain A: A.55, E.70, Q.113, I.117, K.285, K.289 Chain D: D.258 Ligands: PPK.35, K.38, SAM.40, ADN.41 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain A Water bridges: D:A.259, A:K.289, A:K.289, A:K.289 Hydrogen bonds: A:E.70, A:Q.113 Salt bridges: A:K.289

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

PPK.2: 18 residues within 4Å: Chain A: 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: MET.1, MG.3, MG.4, K.5, SAM.7, ADN.8 14 PLIP interactions: 7 interactions with chain D, 7 interactions with chain A Hydrogen bonds: D:A.281, D:K.285, D:K.285, A:R.264, A:R.264, A:K.265 Water bridges: D:D.134, D:D.134, D:D.291, D:D.291, A:K.181 Salt bridges: A:H.29, A:K.181, A:K.265 PPK.13: 18 residues within 4Å: Chain B: H.29, D.31, K.181, D.258, R.264, K.265 Chain C: E.57, D.134, G.280, A.281, K.285, D.291 Ligands: MET.12, MG.14, MG.15, K.16, SAM.18, ADN.19 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:R.264, B:R.264, B:K.265, C:E.57, C:A.281, C:K.285, C:K.285 Water bridges: B:K.181 Salt bridges: B:H.29, B:K.181, B:K.265 PPK.24: 18 residues within 4Å: Chain B: E.57, D.134, G.280, A.281, K.285, D.291 Chain C: H.29, D.31, K.181, D.258, R.264, K.265 Ligands: MET.23, MG.25, MG.26, K.27, SAM.29, ADN.30 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:R.264, C:R.264, C:K.265, B:E.57, B:A.281, B:K.285, B:K.285 Water bridges: C:K.181 Salt bridges: C:H.29, C:K.181, C:K.265 PPK.35: 18 residues within 4Å: Chain A: 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: MET.34, MG.36, MG.37, K.38, SAM.40, ADN.41 14 PLIP interactions: 7 interactions with chain A, 7 interactions with chain D Hydrogen bonds: A:A.281, A:K.285, A:K.285, D:R.264, D:R.264, D:K.265 Water bridges: A:D.134, A:D.134, A:D.291, A:D.291, D:K.181 Salt bridges: D:H.29, D:K.181, D:K.265

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.31, R.264, K.265 Ligands: PPK.2, K.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.31, H2O.2, H2O.10 MG.4: 3 residues within 4Å: Chain A: K.265 Chain D: D.291 Ligands: PPK.2 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain B: D.31, R.264, K.265 Ligands: PPK.13, K.16 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.31, H2O.22, H2O.30 MG.15: 3 residues within 4Å: Chain B: K.265 Chain C: D.291 Ligands: PPK.13 No protein-ligand interaction detected (PLIP) MG.25: 5 residues within 4Å: Chain C: D.31, R.264, K.265 Ligands: PPK.24, K.27 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.31, H2O.42, H2O.50 MG.26: 3 residues within 4Å: Chain B: D.291 Chain C: K.265 Ligands: PPK.24 No protein-ligand interaction detected (PLIP) MG.36: 5 residues within 4Å: Chain D: D.31, R.264, K.265 Ligands: PPK.35, K.38 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.31, H2O.61, H2O.70 MG.37: 3 residues within 4Å: Chain A: D.291 Chain D: K.265 Ligands: PPK.35 No protein-ligand interaction detected (PLIP)

8 x K: POTASSIUM ION(Non-covalent)

K.5: 6 residues within 4Å: Chain A: D.258, A.259 Chain D: E.57 Ligands: MET.1, PPK.2, MG.3 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:D.258, A:A.259, D:E.57, H2O.15 K.6: 4 residues within 4Å: Chain A: M.138, F.139, H.277, G.278 No protein-ligand interaction detected (PLIP) K.16: 6 residues within 4Å: Chain B: D.258, A.259 Chain C: E.57 Ligands: MET.12, PPK.13, MG.14 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:D.258, B:A.259, C:E.57, H2O.35 K.17: 4 residues within 4Å: Chain B: M.138, F.139, H.277, G.278 No protein-ligand interaction detected (PLIP) K.27: 6 residues within 4Å: Chain B: E.57 Chain C: D.258, A.259 Ligands: MET.23, PPK.24, MG.25 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:D.258, C:A.259, B:E.57, H2O.55 K.28: 4 residues within 4Å: Chain C: M.138, F.139, H.277, G.278 No protein-ligand interaction detected (PLIP) K.38: 6 residues within 4Å: Chain A: E.57 Chain D: D.258, A.259 Ligands: MET.34, PPK.35, MG.36 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:D.258, D:A.259, A:E.57, H2O.75 K.39: 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.7: 21 residues within 4Å: Chain A: 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: MET.1, PPK.2, ADN.8 20 PLIP interactions: 10 interactions with chain A, 9 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: A:D.179, A:S.247, A:R.249, A:D.258, D:E.70, D:E.70, D:Q.113 Water bridges: A:S.206, A:S.247, A:A.259, D:I.117, D:I.117, D:K.289, D:K.289 Salt bridges: A:D.258, D:D.134, D:K.289 pi-Stacking: A:F.250, A:F.250 Hydrophobic interactions: M.1 SAM.18: 21 residues within 4Å: Chain B: H.29, P.30, D.179, K.181, S.247, R.249, F.250, I.252, D.258 Chain C: A.55, E.70, Q.113, D.116, I.117, G.133, D.134, K.289, I.322 Ligands: MET.12, PPK.13, ADN.19 21 PLIP interactions: 10 interactions with chain B, 11 interactions with chain C Hydrogen bonds: B:D.179, B:S.247, B:R.249, B:D.258, C:E.70, C:E.70, C:E.70, C:Q.113 Water bridges: B:S.206, B:S.247, B:A.259, C:I.117, C:I.117, C:D.134, C:K.289, C:K.289 Salt bridges: B:D.258, C:D.134, C:K.289 pi-Stacking: B:F.250, B:F.250 SAM.29: 21 residues within 4Å: Chain B: A.55, E.70, Q.113, D.116, I.117, G.133, D.134, K.289, I.322 Chain C: H.29, P.30, D.179, K.181, S.247, R.249, F.250, I.252, D.258 Ligands: MET.23, PPK.24, ADN.30 22 PLIP interactions: 10 interactions with chain C, 11 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: C:D.179, C:S.247, C:R.249, C:D.258, B:E.70, B:E.70, B:E.70, B:Q.113 Water bridges: C:S.206, C:S.247, C:A.259, B:I.117, B:I.117, B:D.134, B:K.289, B:K.289 Salt bridges: C:D.258, B:D.134, B:K.289 pi-Stacking: C:F.250, C:F.250 Hydrophobic interactions: M.23 SAM.40: 21 residues within 4Å: Chain A: 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: MET.34, PPK.35, ADN.41 20 PLIP interactions: 10 interactions with chain D, 1 Ligand-Ligand interactions, 9 interactions with chain A Hydrogen bonds: D:D.179, D:S.247, D:R.249, D:D.258, A:E.70, A:E.70, A:Q.113 Water bridges: D:S.206, D:S.247, D:A.259, A:I.117, A:I.117, A:K.289, A:K.289 Salt bridges: D:D.258, A:D.134, A:K.289 pi-Stacking: D:F.250, D:F.250 Hydrophobic interactions: M.34

4 x ADN: ADENOSINE(Non-covalent)

ADN.8: 16 residues within 4Å: Chain A: H.29, P.30, D.179, K.181, S.206, S.247, R.249, F.250, D.258 Chain D: D.116, I.117, D.134, I.322 Ligands: MET.1, PPK.2, SAM.7 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:D.179, A:S.247, A:R.249, A:D.258 Water bridges: A:S.206, A:S.247, D:I.117, D:I.117 pi-Stacking: A:F.250, A:F.250 ADN.19: 16 residues within 4Å: Chain B: H.29, P.30, D.179, K.181, S.206, S.247, R.249, F.250, D.258 Chain C: D.116, I.117, D.134, I.322 Ligands: MET.12, PPK.13, SAM.18 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:D.179, B:S.247, B:R.249, B:D.258 Water bridges: B:S.206, B:S.247, C:I.117, C:I.117, C:D.134 pi-Stacking: B:F.250, B:F.250 ADN.30: 16 residues within 4Å: Chain B: D.116, I.117, D.134, I.322 Chain C: H.29, P.30, D.179, K.181, S.206, S.247, R.249, F.250, D.258 Ligands: MET.23, PPK.24, SAM.29 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:D.179, C:S.247, C:R.249, C:D.258 Water bridges: C:S.206, C:S.247, B:I.117, B:I.117, B:D.134 pi-Stacking: C:F.250, C:F.250 ADN.41: 16 residues within 4Å: Chain A: 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, D.258 Ligands: MET.34, PPK.35, SAM.40 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:D.179, D:S.247, D:R.249, D:D.258 Water bridges: D:S.206, D:S.247, A:I.117, A:I.117 pi-Stacking: D:F.250, D:F.250

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

PEG.9: 4 residues within 4Å: Chain A: K.350, K.351, N.352, F.353 No protein-ligand interaction detected (PLIP) PEG.20: 4 residues within 4Å: Chain B: K.350, K.351, N.352, F.353 No protein-ligand interaction detected (PLIP) PEG.31: 4 residues within 4Å: Chain C: K.350, K.351, N.352, F.353 No protein-ligand interaction detected (PLIP) PEG.42: 4 residues within 4Å: Chain D: K.350, K.351, N.352, F.353 No protein-ligand interaction detected (PLIP)

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

EDO.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.32: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.43: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PG4.11: 11 residues within 4Å: Chain A: L.315, F.333, Y.335 Chain D: F.18, F.20, Q.190, G.193, V.195, W.274, R.313 Ligands: PG4.44 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.313 Water bridges: D:G.275 PG4.22: 11 residues within 4Å: Chain B: L.315, F.333, Y.335 Chain C: F.18, F.20, Q.190, G.193, V.195, W.274, R.313 Ligands: PG4.33 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.313 Water bridges: C:G.275 PG4.33: 11 residues within 4Å: Chain B: F.18, F.20, Q.190, G.193, V.195, W.274, R.313 Chain C: L.315, F.333, Y.335 Ligands: PG4.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.313 Water bridges: B:G.275 PG4.44: 11 residues within 4Å: Chain A: F.18, F.20, Q.190, G.193, V.195, W.274, R.313 Chain D: L.315, F.333, Y.335 Ligands: PG4.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.313 Water bridges: A:G.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murray, B. et al., Crystallography Captures Catalytic Steps in Human Methionine Adenosyltransferase Enzymes. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-03-09

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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