SMTL ID : 7pzz.1

Crystal structure of serine hydroxymethyltransferase, isoform 2 from Arabidopsis thaliana (SHM2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: Q.89, L.93, G.104, V.105 Ligand excluded by PLIP EDO.2: 5 residues within 4Å: Chain A: A.122, L.123, L.124, K.125, R.282 Ligand excluded by PLIP EDO.3: 10 residues within 4Å: Chain A: I.130, M.131, A.132, L.133, D.134, H.143, G.144, T.161, M.162, P.163 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: E.67, Y.74 Chain B: L.135, L.141 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: E.24, D.27, I.28, L.31 Chain B: M.83 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: K.151, I.152, I.157 Chain B: Q.285, A.286, P.289, G.290 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: P.114, F.117 Chain B: P.114, F.117, L.291 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: Q.285, A.286, P.289, G.290 Chain B: K.150, K.151, I.152, I.157 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain B: Q.89, L.93, G.104, V.105, E.280 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain B: T.121, A.122, L.123, L.124, K.125, R.282 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: K.336, Y.338, K.357, D.417, K.421, L.424 Ligand excluded by PLIP EDO.14: 10 residues within 4Å: Chain B: I.130, M.131, A.132, L.133, D.134, H.143, G.144, T.161, M.162, P.163 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: L.141 Chain B: E.67, Y.74 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain C: E.24, D.27, I.28, L.31 Chain D: M.83 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain C: P.136, H.137, G.138, A.196, N.378, T.379 Ligands: EDO.23 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain C: T.121, A.122, L.123, L.124, K.125, R.282 Ligand excluded by PLIP EDO.21: 1 residues within 4Å: Chain C: Q.431 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain C: V.232, D.320 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain C: P.136, H.137, E.168, T.379, V.380, P.381 Ligands: EDO.18 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain C: K.214, V.216, K.266, Y.279 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain C: E.67, Y.74, Y.75 Chain D: L.141 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain C: Q.285, A.286, P.289, G.290 Chain D: I.152 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain D: Q.89, L.93, G.104, V.105 Ligand excluded by PLIP EDO.32: 8 residues within 4Å: Chain D: E.168, N.169, T.170, G.171, L.340, V.341, S.342, G.343 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain C: L.135, L.141 Chain D: E.67, Y.74, F.288 Ligand excluded by PLIP EDO.35: 9 residues within 4Å: Chain D: I.130, M.131, A.132, D.134, H.143, G.144, T.161, M.162, P.163 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain D: A.122, L.123, L.124, K.125, R.282 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain D: K.214, V.216, K.266, Y.279 Ligand excluded by PLIP

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 6 residues within 4Å: Chain A: I.43, P.44, S.45, H.223, R.393 Chain B: Y.75 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain B: I.43, P.44, S.45, H.223, N.376, R.393 Ligand excluded by PLIP CL.29: 6 residues within 4Å: Chain C: I.43, P.44, S.45, H.223, N.376, R.393 Ligand excluded by PLIP CL.38: 6 residues within 4Å: Chain C: Y.75 Chain D: I.43, P.44, S.45, H.223, R.393 Ligand excluded by PLIP

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.9: 6 residues within 4Å: Chain A: R.7, I.11 Chain B: Y.462, Q.465, F.466, P.467 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.465 Salt bridges: B:D.408, A:R.7 pi-Cation interactions: B:F.466

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

PEG.20: 13 residues within 4Å: Chain C: I.130, M.131, A.132, L.133, D.134, L.135, H.140, H.143, G.144, Y.145, T.161, M.162, P.163 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.134, C:L.135, C:H.140, C:M.162 Water bridges: C:T.161 PEG.34: 4 residues within 4Å: Chain C: R.7 Chain D: Q.465, F.466, P.467 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Water bridges: C:R.7, C:S.8, C:S.8, D:Y.462 Hydrogen bonds: D:Q.465

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

SO4.26: 3 residues within 4Å: Chain C: R.199, G.343, G.344 5 PLIP interactions: 5 interactions with chain C Water bridges: C:S.342, C:G.343, C:T.345, C:T.345 Salt bridges: C:R.199 SO4.27: 4 residues within 4Å: Chain C: T.468, E.472, K.473, E.474 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.473, C:E.474 Water bridges: C:T.468, C:F.471, C:F.471 SO4.28: 5 residues within 4Å: Chain C: K.102, W.103, F.237, E.238, R.262 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:F.237 Water bridges: C:R.262, C:R.262 Salt bridges: C:K.102, C:R.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nogues, I. et al., Arabidopsis thaliana serine hydroxymethyltransferases: functions, structures, and perspectives. Plant Physiol Biochem. (2022)

Release Date

2022-08-24

Peptides

Serine hydroxymethyltransferase 2, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Serine hydroxymethyltransferase 2, mitochondrial

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