SMTL ID : 4kh0.1

The R state structure of E. coli ATCase with ATP and Magnesium bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-6-6-mer

Ligands

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

PAL.1: 15 residues within 4Å: Chain A: S.52, T.53, R.54, T.55, R.105, H.134, Q.137, R.167, T.168, R.229, Q.231, P.266, L.267 Chain E: S.80, K.84 25 PLIP interactions: 20 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:T.168 Hydrogen bonds: A:S.52, A:T.53, A:R.54, A:R.54, A:T.55, A:T.55, A:R.105, A:R.105, A:Q.231, A:L.267, E:S.80, E:S.80, E:K.84 Water bridges: A:T.168, A:R.229, A:R.229, A:R.234, A:R.234 Salt bridges: A:R.105, A:H.134, A:R.167, A:R.229, E:K.84, E:K.84 PAL.6: 16 residues within 4Å: Chain C: S.52, T.53, R.54, T.55, R.105, H.134, Q.137, R.167, T.168, R.229, Q.231, P.266, L.267, P.268 Chain K: S.80, K.84 25 PLIP interactions: 21 interactions with chain C, 4 interactions with chain K Hydrophobic interactions: C:T.168, C:P.266 Hydrogen bonds: C:S.52, C:T.53, C:R.54, C:R.54, C:T.55, C:T.55, C:R.105, C:R.105, C:Q.231, C:L.267, K:S.80, K:S.80 Water bridges: C:R.167, C:R.167, C:R.229, C:R.229, C:E.233 Salt bridges: C:R.105, C:H.134, C:R.167, C:R.229, K:K.84, K:K.84 PAL.11: 15 residues within 4Å: Chain E: S.52, T.53, R.54, T.55, R.105, H.134, Q.137, R.167, T.168, R.229, Q.231, P.266, L.267 Chain I: S.80, K.84 25 PLIP interactions: 20 interactions with chain E, 5 interactions with chain I Hydrophobic interactions: E:T.168 Hydrogen bonds: E:S.52, E:T.53, E:R.54, E:R.54, E:T.55, E:T.55, E:R.105, E:R.105, E:Q.231, E:L.267, I:S.80, I:S.80, I:K.84 Water bridges: E:T.168, E:R.229, E:R.229, E:R.234, E:R.234 Salt bridges: E:R.105, E:H.134, E:R.167, E:R.229, I:K.84, I:K.84 PAL.16: 16 residues within 4Å: Chain C: S.80, K.84 Chain G: S.52, T.53, R.54, T.55, R.105, H.134, Q.137, R.167, T.168, R.229, Q.231, P.266, L.267, P.268 25 PLIP interactions: 21 interactions with chain G, 4 interactions with chain C Hydrophobic interactions: G:T.168, G:P.266 Hydrogen bonds: G:S.52, G:T.53, G:R.54, G:R.54, G:T.55, G:T.55, G:R.105, G:R.105, G:Q.231, G:L.267, C:S.80, C:S.80 Water bridges: G:R.167, G:R.167, G:R.229, G:R.229, G:E.233 Salt bridges: G:R.105, G:H.134, G:R.167, G:R.229, C:K.84, C:K.84 PAL.21: 15 residues within 4Å: Chain A: S.80, K.84 Chain I: S.52, T.53, R.54, T.55, R.105, H.134, Q.137, R.167, T.168, R.229, Q.231, P.266, L.267 25 PLIP interactions: 20 interactions with chain I, 5 interactions with chain A Hydrophobic interactions: I:T.168 Hydrogen bonds: I:S.52, I:T.53, I:R.54, I:R.54, I:T.55, I:T.55, I:R.105, I:R.105, I:Q.231, I:L.267, A:S.80, A:S.80, A:K.84 Water bridges: I:T.168, I:R.229, I:R.229, I:R.234, I:R.234 Salt bridges: I:R.105, I:H.134, I:R.167, I:R.229, A:K.84, A:K.84 PAL.26: 16 residues within 4Å: Chain G: S.80, K.84 Chain K: S.52, T.53, R.54, T.55, R.105, H.134, Q.137, R.167, T.168, R.229, Q.231, P.266, L.267, P.268 25 PLIP interactions: 21 interactions with chain K, 4 interactions with chain G Hydrophobic interactions: K:T.168, K:P.266 Hydrogen bonds: K:S.52, K:T.53, K:R.54, K:R.54, K:T.55, K:T.55, K:R.105, K:R.105, K:Q.231, K:L.267, G:S.80, G:S.80 Water bridges: K:R.167, K:R.167, K:R.229, K:R.229, K:E.233 Salt bridges: K:R.105, K:H.134, K:R.167, K:R.229, G:K.84, G:K.84

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain B: C.109, C.114, C.138, C.141 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.109, B:C.114, B:C.138, B:C.141 ZN.7: 4 residues within 4Å: Chain D: C.109, C.114, C.138, C.141 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.109, D:C.114, D:C.138, D:C.141 ZN.12: 4 residues within 4Å: Chain F: C.109, C.114, C.138, C.141 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.109, F:C.114, F:C.138, F:C.141 ZN.17: 4 residues within 4Å: Chain H: C.109, C.114, C.138, C.141 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.109, H:C.114, H:C.138, H:C.141 ZN.22: 4 residues within 4Å: Chain J: C.109, C.114, C.138, C.141 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.109, J:C.114, J:C.138, J:C.141 ZN.27: 4 residues within 4Å: Chain L: C.109, C.114, C.138, C.141 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.109, L:C.114, L:C.138, L:C.141

12 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 14 residues within 4Å: Chain B: A.11, I.12, V.17, D.19, H.20, K.60, N.84, I.86, Y.89, V.91, K.94 Chain D: K.6 Ligands: ATP.4, MG.5 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:I.12, B:D.19, B:K.60, B:T.82, B:T.82, B:Y.89 Water bridges: B:K.94, B:K.94, D:K.6, D:K.6 Salt bridges: B:H.20, B:K.94, B:K.94, B:K.94, D:K.6, D:K.6 ATP.4: 18 residues within 4Å: Chain B: D.19, H.20, T.43, G.45, L.48, P.49, S.50, G.51, E.52, K.56, K.60 Chain D: K.6, L.7, Q.8, V.9, T.43 Ligands: ATP.3, MG.5 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain D Hydrogen bonds: B:D.19, B:G.51, B:E.52, B:K.60, B:K.60, D:Q.8 Salt bridges: B:H.20, B:K.56, B:K.56, B:K.56, D:K.6, D:K.6 Water bridges: D:K.6, D:K.6 ATP.8: 16 residues within 4Å: Chain B: N.5, K.6, L.7 Chain D: A.11, I.12, V.17, D.19, H.20, K.60, N.84, I.86, Y.89, V.91, K.94 Ligands: ATP.9, MG.10 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:I.12, D:D.19, D:K.60, D:Y.89, B:N.5 Water bridges: D:K.94, D:K.94 Salt bridges: D:H.20, D:K.94, D:K.94, D:K.94, B:K.6, B:K.6 ATP.9: 15 residues within 4Å: Chain B: K.6, Q.8, V.9, E.10 Chain D: H.20, L.48, P.49, S.50, G.51, E.52, K.56, L.58, K.60 Ligands: ATP.8, MG.10 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:G.51, D:E.52, D:K.60, D:K.60, B:E.10 Salt bridges: D:H.20, D:K.56, D:K.56, D:K.56, B:K.6, B:K.6 ATP.13: 14 residues within 4Å: Chain F: A.11, I.12, V.17, D.19, H.20, K.60, N.84, I.86, Y.89, V.91, K.94 Chain H: K.6 Ligands: ATP.14, MG.15 16 PLIP interactions: 12 interactions with chain F, 4 interactions with chain H Hydrogen bonds: F:I.12, F:D.19, F:K.60, F:T.82, F:T.82, F:Y.89 Water bridges: F:K.94, F:K.94, H:K.6, H:K.6 Salt bridges: F:H.20, F:K.94, F:K.94, F:K.94, H:K.6, H:K.6 ATP.14: 18 residues within 4Å: Chain F: D.19, H.20, T.43, G.45, L.48, P.49, S.50, G.51, E.52, K.56, K.60 Chain H: K.6, L.7, Q.8, V.9, T.43 Ligands: ATP.13, MG.15 14 PLIP interactions: 9 interactions with chain F, 5 interactions with chain H Hydrogen bonds: F:D.19, F:G.51, F:E.52, F:K.60, F:K.60, H:Q.8 Salt bridges: F:H.20, F:K.56, F:K.56, F:K.56, H:K.6, H:K.6 Water bridges: H:K.6, H:K.6 ATP.18: 16 residues within 4Å: Chain F: N.5, K.6, L.7 Chain H: A.11, I.12, V.17, D.19, H.20, K.60, N.84, I.86, Y.89, V.91, K.94 Ligands: ATP.19, MG.20 13 PLIP interactions: 3 interactions with chain F, 10 interactions with chain H Hydrogen bonds: F:N.5, H:I.12, H:D.19, H:K.60, H:Y.89 Salt bridges: F:K.6, F:K.6, H:H.20, H:K.94, H:K.94, H:K.94 Water bridges: H:K.94, H:K.94 ATP.19: 15 residues within 4Å: Chain F: K.6, Q.8, V.9, E.10 Chain H: H.20, L.48, P.49, S.50, G.51, E.52, K.56, L.58, K.60 Ligands: ATP.18, MG.20 11 PLIP interactions: 3 interactions with chain F, 8 interactions with chain H Hydrogen bonds: F:E.10, H:G.51, H:E.52, H:K.60, H:K.60 Salt bridges: F:K.6, F:K.6, H:H.20, H:K.56, H:K.56, H:K.56 ATP.23: 14 residues within 4Å: Chain J: A.11, I.12, V.17, D.19, H.20, K.60, N.84, I.86, Y.89, V.91, K.94 Chain L: K.6 Ligands: ATP.24, MG.25 16 PLIP interactions: 12 interactions with chain J, 4 interactions with chain L Hydrogen bonds: J:I.12, J:D.19, J:K.60, J:T.82, J:T.82, J:Y.89 Water bridges: J:K.94, J:K.94, L:K.6, L:K.6 Salt bridges: J:H.20, J:K.94, J:K.94, J:K.94, L:K.6, L:K.6 ATP.24: 18 residues within 4Å: Chain J: D.19, H.20, T.43, G.45, L.48, P.49, S.50, G.51, E.52, K.56, K.60 Chain L: K.6, L.7, Q.8, V.9, T.43 Ligands: ATP.23, MG.25 14 PLIP interactions: 5 interactions with chain L, 9 interactions with chain J Hydrogen bonds: L:Q.8, J:D.19, J:G.51, J:E.52, J:K.60, J:K.60 Water bridges: L:K.6, L:K.6 Salt bridges: L:K.6, L:K.6, J:H.20, J:K.56, J:K.56, J:K.56 ATP.28: 16 residues within 4Å: Chain J: N.5, K.6, L.7 Chain L: A.11, I.12, V.17, D.19, H.20, K.60, N.84, I.86, Y.89, V.91, K.94 Ligands: ATP.29, MG.30 13 PLIP interactions: 10 interactions with chain L, 3 interactions with chain J Hydrogen bonds: L:I.12, L:D.19, L:K.60, L:Y.89, J:N.5 Water bridges: L:K.94, L:K.94 Salt bridges: L:H.20, L:K.94, L:K.94, L:K.94, J:K.6, J:K.6 ATP.29: 15 residues within 4Å: Chain J: K.6, Q.8, V.9, E.10 Chain L: H.20, L.48, P.49, S.50, G.51, E.52, K.56, L.58, K.60 Ligands: ATP.28, MG.30 11 PLIP interactions: 8 interactions with chain L, 3 interactions with chain J Hydrogen bonds: L:G.51, L:E.52, L:K.60, L:K.60, J:E.10 Salt bridges: L:H.20, L:K.56, L:K.56, L:K.56, J:K.6, J:K.6

6 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain B: H.20 Chain D: K.6 Ligands: ATP.3, ATP.4 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain D: H.20 Ligands: ATP.8, ATP.9 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain F: H.20 Chain H: K.6 Ligands: ATP.13, ATP.14 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain H: H.20 Ligands: ATP.18, ATP.19 No protein-ligand interaction detected (PLIP) MG.25: 4 residues within 4Å: Chain J: H.20 Chain L: K.6 Ligands: ATP.23, ATP.24 No protein-ligand interaction detected (PLIP) MG.30: 3 residues within 4Å: Chain L: H.20 Ligands: ATP.28, ATP.29 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cockrell, G.M. et al., New Paradigm for Allosteric Regulation of Escherichia coli Aspartate Transcarbamoylase. Biochemistry (2013)

Release Date

2013-11-27

Peptides

Aspartate carbamoyltransferase: ACEGIK
Aspartate carbamoyltransferase regulatory chain: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
A

G
C

I
A

K
C

B
B

D
D

F
B

H
D

J
B

L
D

Aspartate carbamoyltransferase

Aspartate carbamoyltransferase regulatory chain

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