SMTL ID : 2ipo.1

E. coli Aspartate Transcarbamoylase complexed with N-phosphonacetyl-L-asparagine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-6-6-mer

Ligands

6 x 1IP: N~2~-(PHOSPHONOACETYL)-L-ASPARAGINE(Non-covalent)

1IP.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: 3 interactions with chain E, 22 interactions with chain A Hydrogen bonds: E:S.80, E:K.84, A:A.51, A:S.52, A:T.53, A:R.54, A:T.55, A:T.55, A:R.105, A:R.105, A:R.229, A:R.229, A:Q.231, A:L.267 Salt bridges: E:K.84, A:R.105, A:H.134, A:R.167 Hydrophobic interactions: A:T.168, A:P.266 Water bridges: A:R.54, A:R.167, A:R.234, A:R.234, A:R.234 1IP.5: 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 Chain K: S.80, K.84 Ligands: MAE.6 26 PLIP interactions: 23 interactions with chain C, 3 interactions with chain K Hydrophobic interactions: C:T.168, C:P.266 Hydrogen bonds: C:S.52, C:T.53, C:T.53, C:T.53, C:R.54, C:R.54, C:T.55, C:R.105, C:R.105, C:R.229, C:R.229, C:Q.231, C:L.267, K:S.80, K:K.84 Water bridges: C:R.167, C:T.168, C:R.229, C:R.234, C:R.234 Salt bridges: C:R.105, C:H.134, C:R.167, K:K.84 1IP.9: 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: 22 interactions with chain E, 3 interactions with chain I Hydrophobic interactions: E:T.168, E:P.266 Hydrogen bonds: E:A.51, E:S.52, E:T.53, E:R.54, E:T.55, E:T.55, E:R.105, E:R.105, E:R.229, E:R.229, E:Q.231, E:L.267, I:S.80, I:K.84 Water bridges: E:R.54, E:R.167, E:R.234, E:R.234, E:R.234 Salt bridges: E:R.105, E:H.134, E:R.167, I:K.84 1IP.13: 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 Ligands: MAE.14 26 PLIP interactions: 3 interactions with chain C, 23 interactions with chain G Hydrogen bonds: C:S.80, C:K.84, G:S.52, G:T.53, G:T.53, G:T.53, G:R.54, G:R.54, G:T.55, G:R.105, G:R.105, G:R.229, G:R.229, G:Q.231, G:L.267 Salt bridges: C:K.84, G:R.105, G:H.134, G:R.167 Hydrophobic interactions: G:T.168, G:P.266 Water bridges: G:R.167, G:T.168, G:R.229, G:R.234, G:R.234 1IP.17: 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: 22 interactions with chain I, 3 interactions with chain A Hydrophobic interactions: I:T.168, I:P.266 Hydrogen bonds: I:A.51, I:S.52, I:T.53, I:R.54, I:T.55, I:T.55, I:R.105, I:R.105, I:R.229, I:R.229, I:Q.231, I:L.267, A:S.80, A:K.84 Water bridges: I:R.54, I:R.167, I:R.234, I:R.234, I:R.234 Salt bridges: I:R.105, I:H.134, I:R.167, A:K.84 1IP.21: 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 Ligands: MAE.22 26 PLIP interactions: 23 interactions with chain K, 3 interactions with chain G Hydrophobic interactions: K:T.168, K:P.266 Hydrogen bonds: K:S.52, K:T.53, K:T.53, K:T.53, K:R.54, K:R.54, K:T.55, K:R.105, K:R.105, K:R.229, K:R.229, K:Q.231, K:L.267, G:S.80, G:K.84 Water bridges: K:R.167, K:T.168, K:R.229, K:R.234, K:R.234 Salt bridges: K:R.105, K:H.134, K:R.167, G:K.84

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 10 residues within 4Å: Chain A: F.48, E.50, A.51, S.52, R.56, S.74 Chain E: G.72, F.73, N.78, T.79 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: E:T.79, A:F.48 Hydrogen bonds: A:S.52, A:S.52, A:R.56, A:S.74 MPD.7: 3 residues within 4Å: Chain C: K.232, Y.240 Chain I: P.237 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain C Hydrophobic interactions: I:P.237, C:K.232, C:Y.240, C:Y.240 MPD.10: 10 residues within 4Å: Chain E: F.48, E.50, A.51, S.52, R.56, S.74 Chain I: G.72, F.73, N.78, T.79 6 PLIP interactions: 1 interactions with chain I, 5 interactions with chain E Hydrophobic interactions: I:T.79, E:F.48 Hydrogen bonds: E:S.52, E:S.52, E:R.56, E:S.74 MPD.15: 3 residues within 4Å: Chain A: P.237 Chain G: K.232, Y.240 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain A Hydrophobic interactions: G:K.232, G:Y.240, G:Y.240, A:P.237 MPD.18: 10 residues within 4Å: Chain A: G.72, F.73, N.78, T.79 Chain I: F.48, E.50, A.51, S.52, R.56, S.74 6 PLIP interactions: 5 interactions with chain I, 1 interactions with chain A Hydrophobic interactions: I:F.48, A:T.79 Hydrogen bonds: I:S.52, I:S.52, I:R.56, I:S.74 MPD.23: 3 residues within 4Å: Chain E: P.237 Chain K: K.232, Y.240 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain K Hydrophobic interactions: E:P.237, K:K.232, K:Y.240, K:Y.240

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.11: 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.16: 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.19: 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.24: 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 MAE: MALEIC ACID(Non-covalent)

MAE.4: 5 residues within 4Å: Chain C: P.3, L.4, K.7, D.14, D.19 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.7 MAE.6: 9 residues within 4Å: Chain C: R.54, T.55, H.134, Q.137, L.140, P.266, A.289, R.296 Ligands: 1IP.5 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:R.54, C:L.140 Hydrogen bonds: C:Q.137, C:Q.137, C:P.266 Water bridges: C:A.289, C:A.289 Salt bridges: C:H.134, C:R.296 MAE.12: 5 residues within 4Å: Chain G: P.3, L.4, K.7, D.14, D.19 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:K.7 MAE.14: 9 residues within 4Å: Chain G: R.54, T.55, H.134, Q.137, L.140, P.266, A.289, R.296 Ligands: 1IP.13 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:R.54, G:L.140 Hydrogen bonds: G:Q.137, G:Q.137, G:P.266 Water bridges: G:A.289, G:A.289 Salt bridges: G:H.134, G:R.296 MAE.20: 5 residues within 4Å: Chain K: P.3, L.4, K.7, D.14, D.19 1 PLIP interactions: 1 interactions with chain K Salt bridges: K:K.7 MAE.22: 9 residues within 4Å: Chain K: R.54, T.55, H.134, Q.137, L.140, P.266, A.289, R.296 Ligands: 1IP.21 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:R.54, K:L.140 Hydrogen bonds: K:Q.137, K:Q.137, K:P.266 Water bridges: K:A.289, K:A.289 Salt bridges: K:H.134, K:R.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cardia, J.P. et al., Use of L-asparagine and N-phosphonacetyl-L-asparagine to investigate the linkage of catalysis and homotropic cooperativity in E. coli aspartate transcarbomoylase. Proteins (2008)

Release Date

2007-08-28

Peptides

Aspartate carbamoyltransferase catalytic chain: 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 catalytic chain

Aspartate carbamoyltransferase regulatory chain

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