SMTL ID : 9rwd.1

High-resolution structure of human SHMT2 with covalently bound PLP (internal aldimine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: Q.111, P.112, Y.113, R.258, S.259, H.300, A.303 Chain B: H.300 Ligand excluded by PLIP EDO.2: 10 residues within 4Å: Chain A: G.135, L.136, D.137, L.138, H.146, G.147, Y.148, S.164, M.165, P.166 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: K.168, L.169, N.170, P.171, D.177, Q.180 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: S.20, L.21, S.22, W.29, H.476 Chain B: E.58 Ligand excluded by PLIP EDO.8: 12 residues within 4Å: Chain A: H.300 Chain B: V.110, Q.111, P.112, Y.113, S.114, R.258, S.259, G.260, H.300, A.303, I.304 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: E.58 Chain B: S.20, L.21, S.22, W.29, H.476 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain B: K.36, D.37, C.40, R.466, D.474, E.475 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain B: A.467, F.468 Ligand excluded by PLIP EDO.12: 11 residues within 4Å: Chain B: I.133, M.134, G.135, L.136, D.137, H.146, G.147, Y.148, S.164, M.165, P.166 Ligand excluded by PLIP EDO.14: 10 residues within 4Å: Chain C: M.134, G.135, L.136, D.137, H.146, G.147, Y.148, S.164, M.165, P.166 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain C: Q.463, F.464, R.466, A.467 Ligand excluded by PLIP EDO.16: 12 residues within 4Å: Chain C: V.110, Q.111, P.112, Y.113, S.114, R.258, S.259, G.260, H.300, A.303, I.304 Chain D: H.300 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain C: W.15, G.17, E.19, S.24 Chain D: S.53, A.55, Q.313 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain C: P.117, L.120, L.295, Q.296 Chain D: P.117, L.120, L.295 Ligand excluded by PLIP EDO.20: 10 residues within 4Å: Chain D: M.134, G.135, L.136, D.137, H.146, G.147, Y.148, S.164, M.165, P.166 Ligand excluded by PLIP EDO.21: 10 residues within 4Å: Chain C: H.300 Chain D: Q.111, P.112, Y.113, S.114, R.258, S.259, G.260, H.300, A.303 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain D: K.168, L.169, N.170, P.171, D.177, Q.180 Ligand excluded by PLIP

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 5 residues within 4Å: Chain A: Q.407, R.409, F.468, P.469 Ligands: PEG.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.409, A:R.409 Water bridges: A:Q.407, A:D.412

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

PEG.6: 5 residues within 4Å: Chain A: Q.407, A.467, F.468, P.469 Ligands: TRS.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.412 PEG.23: 9 residues within 4Å: Chain C: S.53, R.54, A.55, Q.313 Chain D: W.15, G.17, Q.18, E.19, S.24 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.54, C:A.55, D:E.19 Water bridges: C:K.312, C:Q.313, C:Q.313

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

NA.7: 2 residues within 4Å: Chain A: K.431, T.434 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.431 NA.13: 2 residues within 4Å: Chain B: K.431, T.434 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.434 Water bridges: B:T.434 NA.19: 2 residues within 4Å: Chain C: K.431, T.434 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.434 NA.24: 2 residues within 4Å: Chain D: K.431, T.434 2 PLIP interactions: 2 interactions with chain D Water bridges: D:K.431, D:T.434

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Warlich, A. et al., High-resolution structure of human SHMT2 with covalently bound PLP (internal aldimine). To Be Published

Release Date

2025-08-13

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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