SMTL ID : 8aql.1

High-resolution crystal structure of human SHMT2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.23 Å

Oligo State

homo-tetramer

Ligands

4 x PLG: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE](Non-covalent)

PLG.1: 18 residues within 4Å: Chain A: S.48, S.114, G.115, S.116, H.143, T.197, S.198, D.223, A.225, H.226, T.249, H.251, K.252, R.397 Chain B: Y.68, Y.78, G.297, G.298 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.225 Hydrogen bonds: A:S.48, A:G.115, A:S.116, A:S.198, B:Y.68, B:Y.78, B:G.297, B:G.298 Water bridges: A:S.114, A:T.247, A:R.258 Salt bridges: A:H.226, A:H.251, A:K.252, A:R.397 pi-Stacking: A:H.143 PLG.4: 18 residues within 4Å: Chain A: Y.68, Y.78, G.297, G.298 Chain B: S.48, S.114, G.115, S.116, H.143, T.197, S.198, D.223, A.225, H.226, T.249, H.251, K.252, R.397 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.225 Hydrogen bonds: B:S.48, B:G.115, B:S.116, B:S.116, A:Y.68, A:Y.78, A:G.297, A:G.298 Water bridges: B:S.114, B:T.247, B:R.258 Salt bridges: B:H.226, B:H.251, B:K.252, B:R.397 pi-Stacking: B:H.143 PLG.8: 18 residues within 4Å: Chain C: S.48, S.114, G.115, S.116, H.143, T.197, S.198, D.223, A.225, H.226, T.249, H.251, K.252, R.397 Chain D: Y.68, Y.78, G.297, G.298 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:A.225 Hydrogen bonds: C:S.48, C:G.115, C:S.116, D:Y.68, D:Y.78, D:G.298 Water bridges: C:S.114, C:R.258 Salt bridges: C:H.226, C:H.251, C:K.252, C:R.397 pi-Stacking: C:H.143 PLG.11: 18 residues within 4Å: Chain C: Y.68, Y.78, G.297, G.298 Chain D: S.48, S.114, G.115, S.116, H.143, T.197, S.198, D.223, A.225, H.226, T.249, H.251, K.252, R.397 18 PLIP interactions: 13 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:A.225 Hydrogen bonds: D:S.48, D:G.115, D:S.116, C:Y.68, C:Y.113, C:G.297, C:G.298 Water bridges: D:S.114, D:N.119, D:R.258, D:R.397, C:Y.78 Salt bridges: D:H.226, D:H.251, D:K.252, D:R.397 pi-Stacking: D:H.143

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

EDO.2: 5 residues within 4Å: Chain A: R.186, L.187, R.189 Chain C: D.151, K.168 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Water bridges: A:R.189, C:D.151 Hydrogen bonds: C:K.168 EDO.3: 4 residues within 4Å: Chain A: L.138, P.139, N.382, T.383 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.382, A:T.383, A:T.383 Water bridges: A:N.382 EDO.5: 3 residues within 4Å: Chain B: E.211, D.214, E.215 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.211, B:E.215 EDO.6: 1 residues within 4Å: Chain B: Q.438 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.438, B:D.439 EDO.7: 6 residues within 4Å: Chain B: R.186, L.187, R.189 Chain D: D.151, K.168 Ligands: EDO.10 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:K.168, B:R.189 EDO.9: 6 residues within 4Å: Chain C: W.15, G.17, E.19, S.24 Chain D: S.53, Q.313 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.17, C:E.19, D:Q.313 Water bridges: C:G.17, D:S.53 EDO.10: 5 residues within 4Å: Chain B: R.186, R.189, V.216 Chain D: D.151 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.216 EDO.12: 5 residues within 4Å: Chain D: L.169, N.170, P.171, D.177, Q.180 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.177 Water bridges: D:Q.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tran, L.H. et al., High-resolution crystal structure of human SHMT2. To Be Published

Release Date

2022-10-05

Peptides

Serine hydroxymethyltransferase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Serine hydroxymethyltransferase, mitochondrial

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