SMTL ID : 6ypo.2 (1 other biounit)

Arabidopsis aspartate transcarbamoylase bound to UMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-trimer

Ligands

3 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.1: 18 residues within 4Å: Chain A: S.76, R.78, T.79, R.129, H.157, Q.160, R.190, T.191, T.251, R.252, H.290, P.291, L.292, P.293, E.297 Chain C: S.104, A.106, A.107 21 PLIP interactions: 17 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:T.79, A:R.129, A:R.190, A:R.190, A:R.252, A:R.252, A:R.252, A:H.290, C:S.104, C:S.104, C:S.104 Water bridges: A:R.78, A:T.79, A:R.190, A:R.190, A:T.191, A:T.251 Salt bridges: A:R.78, A:R.129, A:H.157 Hydrophobic interactions: C:A.107 U5P.4: 18 residues within 4Å: Chain A: S.104, A.106, A.107 Chain B: S.76, R.78, T.79, R.129, H.157, Q.160, R.190, T.191, T.251, R.252, H.290, P.291, L.292, P.293, E.297 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.79, B:R.129, B:R.190, B:R.190, B:R.252, B:R.252, B:R.252, B:H.290, A:S.104, A:S.104, A:S.104 Water bridges: B:R.78, B:T.79, B:R.190, B:R.190, B:T.191, B:T.251 Salt bridges: B:R.78, B:R.129, B:H.157 Hydrophobic interactions: A:A.107 U5P.7: 18 residues within 4Å: Chain B: S.104, A.106, A.107 Chain C: S.76, R.78, T.79, R.129, H.157, Q.160, R.190, T.191, T.251, R.252, H.290, P.291, L.292, P.293, E.297 21 PLIP interactions: 4 interactions with chain B, 17 interactions with chain C Hydrophobic interactions: B:A.107 Hydrogen bonds: B:S.104, B:S.104, B:S.104, C:T.79, C:R.129, C:R.190, C:R.190, C:R.252, C:R.252, C:R.252, C:H.290 Water bridges: C:R.78, C:T.79, C:R.190, C:R.190, C:T.191, C:T.251 Salt bridges: C:R.78, C:R.129, C:H.157

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: R.37, S.41, Q.169, K.174, L.175, D.176, F.202 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.37, A:R.37, A:S.41, A:Q.169, A:L.175, A:D.176, A:D.176 GOL.3: 8 residues within 4Å: Chain A: E.31, G.32, K.33, E.156, R.193, S.194, Y.197, I.221 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.32, A:K.33, A:E.156, A:E.156 Water bridges: A:E.156 GOL.5: 7 residues within 4Å: Chain B: R.37, S.41, Q.169, K.174, L.175, D.176, F.202 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.37, B:R.37, B:S.41, B:Q.169, B:L.175, B:D.176, B:D.176 GOL.6: 8 residues within 4Å: Chain B: E.31, G.32, K.33, E.156, R.193, S.194, Y.197, I.221 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.32, B:K.33, B:E.156, B:E.156 Water bridges: B:E.156 GOL.8: 7 residues within 4Å: Chain C: R.37, S.41, Q.169, K.174, L.175, D.176, F.202 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.37, C:R.37, C:S.41, C:Q.169, C:L.175, C:D.176, C:D.176 GOL.9: 8 residues within 4Å: Chain C: E.31, G.32, K.33, E.156, R.193, S.194, Y.197, I.221 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.32, C:K.33, C:E.156, C:E.156 Water bridges: C:E.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bellin, L. et al., Mechanisms of feedback inhibition and sequential firing of active sites in plant aspartate transcarbamoylase. Nat Commun (2021)

Release Date

2021-03-03

Peptides

PYRB: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

PYRB

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