SMTL ID : 3l05.1

Crystal structure of N-acetyl-L-ornithine transcarbamylase E92S mutant complexed with carbamyl phosphate and N-succinyl-L-norvaline

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-trimer

Ligands

3 x SN0: N-(3-CARBOXYPROPANOYL)-L-NORVALINE(Non-covalent)

SN0.1: 12 residues within 4Å: Chain A: F.134, E.164, H.200, L.204, N.205, K.272, C.314, L.315, R.318 Chain B: W.97, S.112 Ligands: CP.2 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.134, A:L.204, B:W.97 Hydrogen bonds: A:E.164, A:N.205 Water bridges: A:K.272, A:K.272, A:K.272 Salt bridges: A:H.200, A:K.272, A:R.318 SN0.4: 12 residues within 4Å: Chain B: F.134, E.164, H.200, L.204, N.205, K.272, C.314, L.315, R.318 Chain C: W.97, S.112 Ligands: CP.5 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.134, B:L.204, C:W.97 Hydrogen bonds: B:E.164, B:N.205 Water bridges: B:E.164, B:E.164, B:K.272, B:K.272 Salt bridges: B:H.200, B:K.272, B:R.318 SN0.7: 12 residues within 4Å: Chain A: W.97, S.112 Chain C: F.134, E.164, H.200, L.204, N.205, K.272, C.314, L.315, R.318 Ligands: CP.8 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.134, C:L.204, A:W.97 Hydrogen bonds: C:E.164, C:N.205 Water bridges: C:K.272, C:K.272, C:K.272 Salt bridges: C:H.200, C:K.272, C:R.318

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

CP.2: 13 residues within 4Å: Chain A: S.69, M.70, R.71, T.72, R.132, H.168, Q.171, C.314, L.315, P.316, R.342 Chain B: W.97 Ligands: SN0.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:M.70, A:R.71, A:T.72, A:T.72, A:R.132, A:Q.171, A:R.342 Water bridges: A:Q.171 Salt bridges: A:R.71, A:R.132 CP.5: 13 residues within 4Å: Chain B: S.69, M.70, R.71, T.72, R.132, H.168, Q.171, C.314, L.315, P.316, R.342 Chain C: W.97 Ligands: SN0.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:M.70, B:R.71, B:T.72, B:T.72, B:R.132, B:Q.171, B:R.342 Water bridges: B:Q.171 Salt bridges: B:R.71, B:R.132 CP.8: 13 residues within 4Å: Chain A: W.97 Chain C: S.69, M.70, R.71, T.72, R.132, H.168, Q.171, C.314, L.315, P.316, R.342 Ligands: SN0.7 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:M.70, C:R.71, C:T.72, C:T.72, C:T.72, C:R.132, C:Q.171, C:R.342 Water bridges: C:Q.171 Salt bridges: C:R.71, C:R.132

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

SO4.3: 8 residues within 4Å: Chain A: F.81, H.86 Chain B: F.81, H.86 Chain C: F.81, H.86 Ligands: SO4.6, SO4.9 7 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B, 3 interactions with chain A Salt bridges: C:H.86, B:H.86, A:H.86 Water bridges: B:H.86, B:H.86, A:H.86, A:H.86 SO4.6: 8 residues within 4Å: Chain A: F.81, H.86 Chain B: F.81, H.86 Chain C: F.81, H.86 Ligands: SO4.3, SO4.9 8 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B, 3 interactions with chain A Water bridges: C:H.86, B:H.86, B:H.86, A:H.86, A:H.86 Salt bridges: C:H.86, B:H.86, A:H.86 SO4.9: 8 residues within 4Å: Chain A: F.81, H.86 Chain B: F.81, H.86 Chain C: F.81, H.86 Ligands: SO4.3, SO4.6 8 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B, 3 interactions with chain A Water bridges: C:H.86, B:H.86, B:H.86, A:H.86, A:H.86 Salt bridges: C:H.86, B:H.86, A:H.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, D. et al., A single mutation in the active site swaps the substrate specificity of N-acetyl-L-ornithine transcarbamylase and N-succinyl-L-ornithine transcarbamylase. Protein Sci. (2007)

Release Date

2010-03-31

Peptides

N-acetylornithine carbamoyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

N-acetylornithine carbamoyltransferase