SMTL ID : 4kh1.1

The R state structure of E. coli ATCase with CTP,UTP, and Magnesium bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-6-6-mer

Ligands

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

PAL.1: 16 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, P.268 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.7: 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 26 PLIP interactions: 5 interactions with chain K, 21 interactions with chain C Hydrogen bonds: K:S.80, K:S.80, K:K.84, 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 Salt bridges: K:K.84, K:K.84, C:R.105, C:H.134, C:R.167, C:R.229 Hydrophobic interactions: C:T.168, C:P.266 Water bridges: C:R.167, C:T.168, C:R.229, C:R.229, C:R.229 PAL.12: 16 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, P.268 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.18: 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 26 PLIP interactions: 21 interactions with chain G, 5 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, C:K.84 Water bridges: G:R.167, G:T.168, G:R.229, G:R.229, G:R.229 Salt bridges: G:R.105, G:H.134, G:R.167, G:R.229, C:K.84, C:K.84 PAL.23: 16 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, P.268 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.29: 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 26 PLIP interactions: 21 interactions with chain K, 5 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, G:K.84 Water bridges: K:R.167, K:T.168, K:R.229, K:R.229, K:R.229 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.8: 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.13: 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.19: 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.24: 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.30: 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

6 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.3: 15 residues within 4Å: Chain B: L.7, A.11, I.12, V.17, D.19, H.20, L.58, K.60, N.84, I.86, Y.89, V.91, K.94 Ligands: UTP.4, MG.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.86 Hydrogen bonds: B:I.12, B:K.60, B:K.60, B:Y.89 Salt bridges: B:H.20, B:K.94, B:K.94, B:K.94 CTP.9: 15 residues within 4Å: Chain D: L.7, E.10, A.11, I.12, V.17, D.19, H.20, K.60, N.84, I.86, Y.89, V.91, K.94 Ligands: UTP.10, MG.11 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.86 Hydrogen bonds: D:I.12, D:K.60, D:Y.89 Water bridges: D:D.19, D:H.20, D:K.56 Salt bridges: D:H.20, D:K.94, D:K.94, D:K.94 CTP.14: 15 residues within 4Å: Chain F: L.7, A.11, I.12, V.17, D.19, H.20, L.58, K.60, N.84, I.86, Y.89, V.91, K.94 Ligands: UTP.15, MG.16 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:I.86 Hydrogen bonds: F:I.12, F:K.60, F:K.60, F:Y.89 Salt bridges: F:H.20, F:K.94, F:K.94, F:K.94 CTP.20: 15 residues within 4Å: Chain H: L.7, E.10, A.11, I.12, V.17, D.19, H.20, K.60, N.84, I.86, Y.89, V.91, K.94 Ligands: UTP.21, MG.22 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:I.86 Hydrogen bonds: H:I.12, H:K.60, H:Y.89 Water bridges: H:D.19, H:H.20, H:K.56 Salt bridges: H:H.20, H:K.94, H:K.94, H:K.94 CTP.25: 15 residues within 4Å: Chain J: L.7, A.11, I.12, V.17, D.19, H.20, L.58, K.60, N.84, I.86, Y.89, V.91, K.94 Ligands: UTP.26, MG.27 9 PLIP interactions: 9 interactions with chain J Hydrophobic interactions: J:I.86 Hydrogen bonds: J:I.12, J:K.60, J:K.60, J:Y.89 Salt bridges: J:H.20, J:K.94, J:K.94, J:K.94 CTP.31: 15 residues within 4Å: Chain L: L.7, E.10, A.11, I.12, V.17, D.19, H.20, K.60, N.84, I.86, Y.89, V.91, K.94 Ligands: UTP.32, MG.33 11 PLIP interactions: 11 interactions with chain L Hydrophobic interactions: L:I.86 Hydrogen bonds: L:I.12, L:K.60, L:Y.89 Water bridges: L:D.19, L:H.20, L:K.56 Salt bridges: L:H.20, L:K.94, L:K.94, L:K.94

6 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.4: 14 residues within 4Å: Chain B: L.7, Q.8, V.9, H.20, L.48, P.49, S.50, G.51, E.52, K.56, L.58, K.60 Ligands: CTP.3, MG.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.58 Hydrogen bonds: B:Q.8, B:V.9, B:V.9, B:S.50, B:G.51, B:E.52, B:K.60 Water bridges: B:D.19, B:H.20 Salt bridges: B:H.20, B:K.56, B:K.56, B:K.56 UTP.10: 13 residues within 4Å: Chain D: L.7, Q.8, V.9, H.20, P.49, S.50, G.51, E.52, K.56, L.58, K.60 Ligands: CTP.9, MG.11 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:L.58 Hydrogen bonds: D:Q.8, D:V.9, D:V.9, D:G.51, D:E.52, D:E.52, D:K.60 Water bridges: D:K.56, D:K.56 Salt bridges: D:H.20, D:K.56, D:K.56, D:K.56 UTP.15: 14 residues within 4Å: Chain F: L.7, Q.8, V.9, H.20, L.48, P.49, S.50, G.51, E.52, K.56, L.58, K.60 Ligands: CTP.14, MG.16 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:L.58 Hydrogen bonds: F:Q.8, F:V.9, F:V.9, F:S.50, F:G.51, F:E.52, F:K.60 Water bridges: F:D.19, F:H.20 Salt bridges: F:H.20, F:K.56, F:K.56, F:K.56 UTP.21: 13 residues within 4Å: Chain H: L.7, Q.8, V.9, H.20, P.49, S.50, G.51, E.52, K.56, L.58, K.60 Ligands: CTP.20, MG.22 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:L.58 Hydrogen bonds: H:Q.8, H:V.9, H:V.9, H:G.51, H:E.52, H:E.52, H:K.60 Water bridges: H:K.56, H:K.56 Salt bridges: H:H.20, H:K.56, H:K.56, H:K.56 UTP.26: 14 residues within 4Å: Chain J: L.7, Q.8, V.9, H.20, L.48, P.49, S.50, G.51, E.52, K.56, L.58, K.60 Ligands: CTP.25, MG.27 14 PLIP interactions: 14 interactions with chain J Hydrophobic interactions: J:L.58 Hydrogen bonds: J:Q.8, J:V.9, J:V.9, J:S.50, J:G.51, J:E.52, J:K.60 Water bridges: J:D.19, J:H.20 Salt bridges: J:H.20, J:K.56, J:K.56, J:K.56 UTP.32: 13 residues within 4Å: Chain L: L.7, Q.8, V.9, H.20, P.49, S.50, G.51, E.52, K.56, L.58, K.60 Ligands: CTP.31, MG.33 14 PLIP interactions: 14 interactions with chain L Hydrophobic interactions: L:L.58 Hydrogen bonds: L:Q.8, L:V.9, L:V.9, L:G.51, L:E.52, L:E.52, L:K.60 Water bridges: L:K.56, L:K.56 Salt bridges: L:H.20, L:K.56, L:K.56, L:K.56

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.5: 3 residues within 4Å: Chain B: H.20 Ligands: CTP.3, UTP.4 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Ligands: CTP.9, UTP.10 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain F: H.20 Ligands: CTP.14, UTP.15 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Ligands: CTP.20, UTP.21 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain J: H.20 Ligands: CTP.25, UTP.26 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Ligands: CTP.31, UTP.32 No protein-ligand interaction detected (PLIP)

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 5 residues within 4Å: Chain A: Q.196 Chain B: R.130, E.144, F.145, S.146 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.146 Salt bridges: B:R.130 Water bridges: A:Q.196, A:Q.196, A:D.200 PO4.17: 5 residues within 4Å: Chain E: Q.196 Chain F: R.130, E.144, F.145, S.146 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Water bridges: E:Q.196, E:Q.196, E:D.200 Hydrogen bonds: F:S.146 Salt bridges: F:R.130 PO4.28: 5 residues within 4Å: Chain I: Q.196 Chain J: R.130, E.144, F.145, S.146 5 PLIP interactions: 2 interactions with chain J, 3 interactions with chain I Hydrogen bonds: J:S.146 Salt bridges: J:R.130 Water bridges: I:Q.196, I:Q.196, I:D.200

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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