SMTL ID : 3kzo.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x AN0: N-ACETYL-L-NORVALINE(Non-covalent)

AN0.1: 10 residues within 4Å: Chain A: E.164, L.204, N.205, K.272, C.314, L.315, K.322 Chain B: W.97, E.112 Ligands: CP.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.204 Hydrogen bonds: A:N.205 Water bridges: A:N.205, A:K.272 Salt bridges: A:K.272 AN0.5: 10 residues within 4Å: Chain B: E.164, L.204, N.205, K.272, C.314, L.315, K.322 Chain C: W.97, E.112 Ligands: CP.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.204 Hydrogen bonds: B:N.205 Water bridges: B:E.164, B:E.164, B:N.205 Salt bridges: B:K.272 AN0.9: 10 residues within 4Å: Chain A: W.97, E.112 Chain C: E.164, L.204, N.205, K.272, C.314, L.315, K.322 Ligands: CP.10 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.204 Hydrogen bonds: C:N.205 Water bridges: C:N.205, C:K.272 Salt bridges: C:K.272

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

CP.2: 12 residues within 4Å: Chain A: S.69, M.70, R.71, T.72, R.132, H.168, Q.171, C.314, L.315, R.342 Chain B: W.97 Ligands: AN0.1 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:M.70, A:R.71, A:T.72, A:T.72, A:R.132, A:R.132, A:Q.171, A:R.342, B:W.97 Water bridges: A:Q.171 Salt bridges: A:R.71, A:R.132 CP.6: 12 residues within 4Å: Chain B: S.69, M.70, R.71, T.72, R.132, H.168, Q.171, C.314, L.315, R.342 Chain C: W.97 Ligands: AN0.5 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:M.70, B:R.71, B:T.72, B:T.72, B:R.132, B:R.132, B:Q.171, B:R.342, C:W.97 Water bridges: B:Q.171 Salt bridges: B:R.71, B:R.132 CP.10: 12 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, R.342 Ligands: AN0.9 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:M.70, C:R.71, C:T.72, C:T.72, C:T.72, C:R.132, C:R.132, C:Q.171, C:R.342, A:W.97 Water bridges: C:Q.171 Salt bridges: C:R.71, C:R.132

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: S.33, R.34, A.35, R.218 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.34, A:A.35, A:R.218 Water bridges: A:E.248 GOL.7: 4 residues within 4Å: Chain B: S.33, R.34, A.35, R.218 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.34, B:A.35, B:R.218 Water bridges: B:E.248 GOL.11: 4 residues within 4Å: Chain C: S.33, R.34, A.35, R.218 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.34, C:A.35, C:R.218 Water bridges: C:E.248

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

SO4.4: 8 residues within 4Å: Chain A: F.81, H.86 Chain B: F.81, H.86 Chain C: F.81, H.86 Ligands: SO4.8, SO4.12 7 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A, 1 interactions with chain C Water bridges: B:H.86, B:H.86, A:G.85, A:H.86 Salt bridges: B:H.86, A:H.86, C:H.86 SO4.8: 8 residues within 4Å: Chain A: F.81, H.86 Chain B: F.81, H.86 Chain C: F.81, H.86 Ligands: SO4.4, SO4.12 8 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A, 2 interactions with chain C Water bridges: B:G.85, B:H.86, A:H.86, A:H.86, C:H.86 Salt bridges: B:H.86, A:H.86, C:H.86 SO4.12: 8 residues within 4Å: Chain A: F.81, H.86 Chain B: F.81, H.86 Chain C: F.81, H.86 Ligands: SO4.4, SO4.8 8 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A, 2 interactions with chain C Water bridges: B:H.86, B:H.86, A:H.86, A:H.86, C:G.85 Salt bridges: B:H.86, A:H.86, C:H.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, D. et al., Structures of N-acetylornithine transcarbamoylase from Xanthomonas campestris complexed with substrates and substrate analogs imply mechanisms for substrate binding and catalysis. Proteins (2006)

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

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