SMTL ID : 6ysp.1

Arabidopsis aspartate transcarbamoylase complex with PALA and carbamoyl phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-trimer

Ligands

2 x CP: PHOSPHORIC ACID MONO(FORMAMIDE)ESTER(Non-covalent)

CP.1: 12 residues within 4Å: Chain A: S.76, T.77, R.78, T.79, R.80, R.129, H.157, Q.160, P.291, L.292, P.293 Chain C: S.105 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.77, A:R.78, A:R.78, A:T.79, A:T.79, A:R.129, A:H.157, A:Q.160, C:S.105 Water bridges: A:Q.160, A:R.190 Salt bridges: A:R.78, A:R.129 CP.4: 14 residues within 4Å: Chain A: S.105, K.108 Chain B: S.76, T.77, R.78, T.79, R.80, R.129, H.157, Q.160, P.291, L.292, P.293 Ligands: GOL.7 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.76, B:T.77, B:R.78, B:R.78, B:T.79, B:T.79, B:R.129, B:H.157, B:Q.160, A:S.105 Salt bridges: B:R.78, B:R.129, A:K.108

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

SO4.2: 4 residues within 4Å: Chain A: R.252, Q.254, R.255, L.295 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.253, A:R.255 Water bridges: A:E.256 Salt bridges: A:R.252 SO4.5: 7 residues within 4Å: Chain B: G.189, R.190, T.191, T.251, Q.254, R.257 Ligands: GOL.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.190, B:T.191, B:Q.254 Water bridges: B:G.189, B:V.192, B:R.252, B:R.257, B:R.257 Salt bridges: B:R.190, B:R.257

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: I.53, E.54, S.56, S.57, S.58, Q.59, S.60, R.89, L.90 Chain C: G.65 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.54, A:S.57, A:S.60, A:R.89, A:R.89 Water bridges: A:Q.59 GOL.6: 7 residues within 4Å: Chain B: R.37, S.41, Q.169, K.174, L.175, D.176, F.202 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.41, B:Q.169, B:L.175, B:D.176, B:D.176 GOL.7: 11 residues within 4Å: Chain A: K.108 Chain B: R.129, H.157, R.190, T.191, Q.254, P.291, L.292, P.293 Ligands: CP.4, SO4.5 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.129, B:L.292, A:K.108 Water bridges: B:R.252, B:Q.254 GOL.8: 9 residues within 4Å: Chain A: G.65 Chain B: I.53, E.54, S.56, S.57, S.58, Q.59, S.60, R.89 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.56, B:S.60, B:R.89, B:R.89 Water bridges: B:Q.59, B:Q.59 GOL.10: 9 residues within 4Å: Chain B: G.65 Chain C: I.53, E.54, S.56, S.57, S.58, Q.59, S.60, R.89 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:G.65, C:S.60, C:R.89, C:R.89 Water bridges: C:Q.59, C:Q.59 GOL.11: 7 residues within 4Å: Chain C: L.238, M.239, K.271, F.272, I.273, D.275, L.278 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.273, C:I.273

1 x PAL: N-(PHOSPHONACETYL)-L-ASPARTIC ACID(Non-covalent)

PAL.9: 17 residues within 4Å: Chain B: S.105, K.108 Chain C: S.76, T.77, R.78, T.79, R.80, R.129, H.157, Q.160, R.190, T.191, R.252, Q.254, P.291, L.292, P.293 30 PLIP interactions: 25 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:T.191, C:P.291 Hydrogen bonds: C:S.76, C:S.76, C:T.77, C:R.78, C:R.78, C:R.78, C:T.79, C:T.79, C:R.129, C:R.129, C:H.157, C:Q.254, C:L.292, B:S.105, B:S.105, B:K.108 Water bridges: C:R.190, C:T.191, C:T.191, C:R.252, C:R.252, C:R.257 Salt bridges: C:R.129, C:H.157, C:R.190, C:R.252, B:K.108, B:K.108

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
A

B
B

C
C

PYRB

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