SMTL ID : 6fwb.1 (1 other biounit)

Crystal structure of Mat2A at 1.79 Angstron resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

15 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: K.244, A.245, V.246, V.247, P.248 No protein-ligand interaction detected (PLIP) SO4.2: 4 residues within 4Å: Chain A: L.326, I.364, L.409, K.410 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.409 SO4.3: 5 residues within 4Å: Chain A: D.145, G.147, G.339, V.340, S.341 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.341, A:S.341 Water bridges: A:S.341 SO4.4: 5 residues within 4Å: Chain A: K.366, K.367, N.368, F.369, D.370 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.369 Water bridges: A:N.368, A:D.370, A:D.370, A:K.407 SO4.5: 5 residues within 4Å: Chain A: E.164, L.168, V.171, L.172, K.175 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.163, A:Y.251 Salt bridges: A:K.175 SO4.6: 7 residues within 4Å: Chain A: M.154, F.155, Y.287, A.292, H.293, G.294, A.311 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.155, A:G.294 Water bridges: A:F.155, A:Y.287, A:G.296 Salt bridges: A:H.293 SO4.7: 5 residues within 4Å: Chain A: S.111, S.112, K.113, G.114, Q.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.111, A:Q.272 SO4.12: 6 residues within 4Å: Chain A: G.296, A.297, K.301 Chain B: D.47, R.280, K.281 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Water bridges: B:D.47, B:K.281, B:K.281, B:K.281 Salt bridges: B:R.280, B:K.281, A:K.301 Hydrogen bonds: A:A.297 SO4.13: 5 residues within 4Å: Chain B: T.162, E.164, V.171, K.175, P.248 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.164 Water bridges: B:E.163 Salt bridges: B:K.175 SO4.14: 5 residues within 4Å: Chain B: K.244, A.245, V.246, V.247, P.248 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.246 Water bridges: B:A.249, B:A.249 SO4.15: 5 residues within 4Å: Chain B: K.366, K.367, N.368, F.369, D.370 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.368, B:D.370 SO4.16: 4 residues within 4Å: Chain B: E.254, D.255, T.256, I.257 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.256 SO4.17: 3 residues within 4Å: Chain B: S.263, R.265, F.266 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.263 SO4.18: 3 residues within 4Å: Chain B: C.230, L.231, R.265 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.231 Salt bridges: B:R.265 SO4.19: 7 residues within 4Å: Chain A: T.33, F.34 Chain B: S.347, I.348, E.358, R.359, L.362 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.348, B:I.348, B:E.358 Salt bridges: B:R.359

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

PG4.8: 4 residues within 4Å: Chain A: Q.96, R.100, E.101, K.118 No protein-ligand interaction detected (PLIP) PG4.9: 6 residues within 4Å: Chain A: Q.388, R.389, A.392, Y.393, R.398 Ligands: NA.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.392, A:R.398, A:R.398 Water bridges: A:P.385 PG4.20: 13 residues within 4Å: Chain A: A.292, Q.333, F.349 Chain B: F.34, F.36, Y.157, Q.206, V.211, G.289, W.290, G.291, R.329, Y.351 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.157, B:G.291, B:R.329, B:R.329 PG4.21: 6 residues within 4Å: Chain A: F.34, Q.206, W.290, R.329, Y.351 Chain B: F.349 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.206, A:R.329

1 x NA: SODIUM ION(Non-functional Binders)

NA.10: 7 residues within 4Å: Chain A: D.59, P.385, I.386, Y.387, Q.388, R.389 Ligands: PG4.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.385, A:Q.388, A:R.389

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 10 residues within 4Å: Chain B: G.42, E.43, N.177, L.180, A.181, R.184, R.193, P.194, S.196, Y.393 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.43, B:R.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bai, J. et al., Identification of a natural inhibitor of methionine adenosyltransferase 2A regulating one-carbon metabolism in keratinocytes. Ebiomedicine (2019)

Release Date

2019-03-27

Peptides

S-adenosylmethionine synthase isoform type-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

S-adenosylmethionine synthase isoform type-2

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