SMTL ID : 8a5w.2 (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

hetero-7-1-mer

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 C: H.39, R.40, N.236, T.237 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:W.102 Hydrogen bonds: A:G.74, A:C.75, A:S.173, A:Q.194, A:Q.194, C:N.236, C: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, C:H.39, C:R.40 pi-Stacking: A:W.102, A:W.102 E1U.6: 19 residues within 4Å: Chain B: H.67, R.68, N.264, T.265 Chain E: 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 16 PLIP interactions: 5 interactions with chain B, 11 interactions with chain E Hydrogen bonds: B:N.264, B:T.265, B:T.265, E:G.74, E:C.75, E:S.173, E:Q.194 Salt bridges: B:H.67, B:R.68, E:H.330, E:H.330, E:R.331, E:R.337 Hydrophobic interactions: E:W.102 pi-Stacking: E:W.102, E:W.102

1 x U93: (2~{S})-2-[[(~{R})-[[(5~{S})-5-azanyl-6-oxidanylidene-hexyl]amino]-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methyl]amino]-3-phosphonooxy-propanoic acid(Covalent)

U93.2: 24 residues within 4Å: Chain B: P.35, G.36, A.38, G.101, G.102, C.103, W.130, T.179, V.180, D.199, S.201, S.202, G.220, A.221, Q.222, N.224, H.358, R.359, R.365, Y.369 Chain E: H.39, R.40, N.236, T.237 19 PLIP interactions: 5 interactions with chain E, 14 interactions with chain B Hydrogen bonds: E:N.236, E:T.237, E:T.237, B:G.102, B:C.103, B:S.202, B:G.220, B:Q.222, B:N.224 Salt bridges: E:H.39, E:R.40, B:H.358, B:H.358, B:R.359, B:R.365 Hydrophobic interactions: B:W.130, B:Q.222 pi-Stacking: B:W.130, B:W.130

3 x SEP: PHOSPHOSERINE(Non-functional Binders)

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

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

PMP.7: 15 residues within 4Å: Chain D: N.236, T.237 Chain F: 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.5 14 PLIP interactions: 11 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:G.73, F:G.74, F:C.75, F:T.151, F:T.151, F:S.173, F:Q.194, F:K.195, F:K.195, D:N.236, D:T.237, D:T.237 pi-Stacking: F:W.102, F:W.102

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

SO4.8: 5 residues within 4Å: Chain G: H.39, R.40 Chain H: W.102, H.330, R.331 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain H Salt bridges: G:H.39, G:R.40, H:H.330, H:R.331 SO4.9: 4 residues within 4Å: Chain G: W.102, H.330 Chain H: H.39, R.40 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:T.237 Water bridges: H:R.40 Salt bridges: H:H.39, H: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: ACDEFGH
Phosphoserine aminotransferase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

C
C

D
B

E
F

F
A

G
G

H
H

B
E

Phosphoserine aminotransferase

Phosphoserine aminotransferase

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