SMTL ID : 8a5w.4 (3 other biounits)

Crystal structure of the human phosphoserine aminotransferase (PSAT) in complex with O-phosphoserine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

homo-heptamer

Ligands

2 x E1U: (2S)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-phosphonooxy-propanoic acid(Non-covalent)

E1U.1: 17 residues within 4Å: Chain A: G.73, G.74, C.75, W.102, T.151, D.171, S.173, S.174, Q.194, K.195, H.330, R.331, R.337 Chain B: H.39, R.40, N.236, T.237 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.102 Hydrogen bonds: A:G.74, A:C.75, A:S.173, A:Q.194, A:Q.194, B:N.236, B:T.237 Water bridges: A:R.337, A:R.337 Salt bridges: A:K.195, A:H.330, A:H.330, A:R.331, A:R.337, B:H.39, B:R.40 pi-Stacking: A:W.102, A:W.102 E1U.5: 15 residues within 4Å: Chain D: P.7, G.73, G.74, C.75, W.102, N.149, T.151, D.171, S.173, S.174, Q.194, K.195, H.330, R.331, R.337 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.102 Hydrogen bonds: D:G.74, D:C.75, D:S.173, D:Q.194 Salt bridges: D:H.330, D:H.330, D:R.331, D:R.337 pi-Stacking: D:W.102, D:W.102

3 x SEP: PHOSPHOSERINE(Non-functional Binders)

SEP.2: 10 residues within 4Å: Chain A: H.39, R.40 Chain B: P.7, G.8, W.102, T.151, K.195, H.330, R.331, R.337 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.8, B:W.102 Salt bridges: B:H.330, B:R.331, B:R.337, A:H.39, A:R.40 SEP.3: 10 residues within 4Å: Chain C: P.7, G.8, W.102, T.151, V.152, K.195, H.330, R.337 Chain E: H.39, R.40 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:G.8, C:R.337 Salt bridges: C:H.330, C:R.337, E:H.39, E:R.40 SEP.4: 9 residues within 4Å: Chain C: H.39, R.40 Chain E: P.7, W.102, T.151, K.195, H.330, R.337 Ligands: PMP.6 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain E Salt bridges: C:H.39, C:R.40, E:K.195, E:R.331, E:R.337 Hydrogen bonds: E:H.330

1 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PMP.6: 15 residues within 4Å: Chain C: N.236, T.237 Chain E: G.73, G.74, C.75, F.78, W.102, N.149, T.151, D.171, S.173, S.174, Q.194, K.195 Ligands: SEP.4 14 PLIP interactions: 11 interactions with chain E, 3 interactions with chain C Hydrogen bonds: E:G.73, E:G.74, E:C.75, E:T.151, E:T.151, E:S.173, E:Q.194, E:K.195, E:K.195, C:N.236, C:T.237, C:T.237 pi-Stacking: E:W.102, E:W.102

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

SO4.7: 5 residues within 4Å: Chain F: H.39, R.40 Chain G: W.102, H.330, R.331 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain F Salt bridges: G:H.330, G:R.331, F:H.39, F:R.40 SO4.8: 4 residues within 4Å: Chain F: W.102, H.330 Chain G: H.39, R.40 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:T.237 Water bridges: G:R.40 Salt bridges: G:H.39, G:R.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marchesani, F. et al., L-serine biosynthesis in the human central nervous system: Structure and function of phosphoserine aminotransferase. Protein Sci. (2023)

Release Date

2023-03-29

Peptides

Phosphoserine aminotransferase: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
B

D
F

E
A

F
G

G
H

Phosphoserine aminotransferase

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