SMTL ID : 4ktt.1

Structural insights of MAT enzymes: MATa2b complexed with SAM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

hetero-4-2-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: F.334, Y.336 Chain B: Q.191 Chain F: T.324, V.325 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: T.18, F.19 Chain B: S.332, I.333, E.343, R.344, L.347 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: A.163, A.166, E.167, R.170, Y.378 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: E.28, N.162, L.165, A.166, R.169, R.178, P.179, S.181 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain B: D.366, L.367, K.368, K.369, I.371, Y.372, W.388 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain B: A.163, E.167, R.170 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain B: G.64, F.100, D.101, T.104, C.105 Chain C: T.104, C.105 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain B: D.36, G.264, I.267, D.270, G.281, A.282, F.283, S.284 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain B: D.79, Y.80, Q.81 Chain D: V.109 Ligands: EDO.25 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: E.58 Chain B: D.32, D.259, A.260, R.265 Ligands: EDO.13 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: K.286, D.292 Chain B: H.30, K.266 Ligands: EDO.12 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain B: L.138, M.139, F.140, H.278, G.279, G.280, G.281, A.296 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain B: R.193, R.313, G.337, T.338 Chain F: W.313, P.314 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain C: M.139, F.140, T.271, Y.272, A.277, H.278, G.279, A.296 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain C: E.28, Q.37, H.90, Q.373, R.374, Y.378 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain C: F.334, H.335, Y.336, G.337 Chain E: T.324 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: K.103 Chain D: S.96, I.253, Q.257 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain D: D.145, K.308 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain D: Q.340, K.341, E.345 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain B: D.79, Q.81 Chain D: I.72, L.111, E.112, Q.113 Ligands: EDO.11 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain D: R.193, R.313, G.337, T.338 Chain E: W.313, P.314 Ligand excluded by PLIP EDO.27: 9 residues within 4Å: Chain D: L.47, P.51, D.52, A.53, K.54, D.287, Y.288, L.367, K.368 Ligand excluded by PLIP EDO.28: 9 residues within 4Å: Chain A: K.62, T.63 Chain B: A.110, E.112 Chain D: Q.81, R.85, C.105, N.106, V.107 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain E: P.92, I.177, A.189, R.212, K.251, R.282 Ligand excluded by PLIP EDO.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain E: G.245, N.246, Q.287, L.288, R.301 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain E: M.193, N.205, M.206, D.207, K.251 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain F: H.47, H.81 Ligand excluded by PLIP

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

SAM.5: 20 residues within 4Å: Chain A: H.30, P.31, D.180, K.182, S.207, S.248, R.250, F.251, I.253, G.258, D.259 Chain B: A.56, E.71, Q.114, D.117, I.118, G.134, D.135, K.290, I.323 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.180, A:S.248, A:R.250, A:D.259, A:D.259, B:Q.114, B:K.290 Salt bridges: A:D.259, B:D.135, B:K.290 pi-Stacking: A:F.251, A:F.251 Water bridges: B:K.290 SAM.20: 21 residues within 4Å: Chain C: H.30, P.31, D.180, K.182, S.207, S.248, R.250, F.251, I.253, G.258, D.259 Chain D: A.56, E.71, Q.114, D.117, I.118, G.134, D.135, K.290, I.323 Ligands: PO4.21 16 PLIP interactions: 7 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: D:I.118 Hydrogen bonds: D:E.71, D:Q.114, D:K.290, D:K.290, C:D.180, C:S.248, C:R.250, C:G.258, C:D.259, C:D.259 Salt bridges: D:D.135, D:K.290, C:D.259 pi-Stacking: C:F.251, C:F.251

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 8 residues within 4Å: Chain A: H.30, D.32, D.259, R.265, K.266 Chain B: D.135, K.286, D.292 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Water bridges: B:E.58 Salt bridges: B:K.286, A:H.30, A:K.266 Hydrogen bonds: A:D.32, A:D.259, A:R.265 PO4.21: 8 residues within 4Å: Chain C: H.30, D.32, K.182, D.259, K.266 Chain D: D.135, D.292 Ligands: SAM.20 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.32, C:D.259, D:D.292 Salt bridges: C:H.30, C:K.182, C:K.266

1 x MG: MAGNESIUM ION(Non-covalent)

MG.16: 7 residues within 4Å: Chain B: D.32, D.36, L.262, T.263, G.264, R.265, K.266 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.32, B:D.36, B:L.262, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murray, B. et al., Structure and function study of the complex that synthesizes S-adenosylmethionine. IUCrJ (2014)

Release Date

2014-07-16

Peptides

S-adenosylmethionine synthase isoform type-2: ABCD
Methionine adenosyltransferase 2 subunit beta: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

S-adenosylmethionine synthase isoform type-2

Methionine adenosyltransferase 2 subunit beta

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