SMTL ID : 2i6u.1

Crystal Structure of Ornithine Carbamoyltransferase complexed with Carbamoyl Phosphate and L-Norvaline from Mycobacterium tuberculosis (Rv1656) at 2.2 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.34, Q.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.37 Salt bridges: A:R.34 SO4.2: 4 residues within 4Å: Chain A: N.248, S.249, T.274, A.276 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.249, A:S.249, A:S.249, A:T.274 Water bridges: A:N.248, A:R.250, A:R.250, A:D.275 SO4.5: 4 residues within 4Å: Chain B: N.248, S.249, T.274, A.276 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.249, B:S.249 Water bridges: B:R.250 SO4.8: 4 residues within 4Å: Chain C: N.248, S.249, T.274, A.276 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.249, C:S.249, C:S.249 Water bridges: C:R.250 SO4.9: 3 residues within 4Å: Chain C: R.243, N.248, R.250 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.248 Water bridges: C:P.244, C:R.250 Salt bridges: C:R.243

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

CP.3: 12 residues within 4Å: Chain A: S.50, T.51, R.52, T.53, R.101, H.128, Q.131, C.264, L.265, R.292 Chain C: Q.77 Ligands: NVA.4 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.51, A:R.52, A:T.53, A:T.53, A:R.101, A:R.101, A:Q.131, A:R.292, C:Q.77 Water bridges: A:Q.131 Salt bridges: A:R.52, A:R.101 CP.6: 12 residues within 4Å: Chain A: Q.77 Chain B: S.50, T.51, R.52, T.53, R.101, H.128, Q.131, C.264, L.265, R.292 Ligands: NVA.7 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.51, B:R.52, B:T.53, B:T.53, B:R.101, B:Q.131, B:R.292, B:R.292, A:Q.77 Water bridges: B:Q.131 Salt bridges: B:R.52, B:R.101 CP.10: 12 residues within 4Å: Chain B: Q.77 Chain C: S.50, T.51, R.52, T.53, R.101, H.128, Q.131, C.264, L.265, R.292 Ligands: NVA.11 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.51, C:R.52, C:T.53, C:R.101, C:R.101, C:Q.131, C:R.292, C:R.292, B:Q.77 Salt bridges: C:R.52, C:R.101

3 x NVA: NORVALINE(Non-covalent)

NVA.4: 10 residues within 4Å: Chain A: L.123, N.159, N.160, D.224, T.225, S.228, M.229, C.264, L.265 Ligands: CP.3 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.123 Hydrogen bonds: A:N.160, A:N.160, A:D.224, A:M.229 Water bridges: C:R.80 NVA.7: 8 residues within 4Å: Chain B: L.123, H.128, N.160, D.224, S.228, M.229, L.265 Ligands: CP.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.123 Hydrogen bonds: B:N.160, B:N.160, B:D.224, B:M.229 Salt bridges: B:K.48 NVA.11: 12 residues within 4Å: Chain B: R.80 Chain C: L.123, H.128, N.159, N.160, D.224, T.225, S.228, M.229, C.264, L.265 Ligands: CP.10 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain C Water bridges: B:R.80 Hydrophobic interactions: C:L.123 Hydrogen bonds: C:N.159, C:N.160, C:N.160, C:D.224, C:M.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sankaranarayanan, R. et al., The crystal structures of ornithine carbamoyltransferase from Mycobacterium tuberculosis and its ternary complex with carbamoyl phosphate and L-norvaline reveal the enzyme's catalytic mechanism. J.Mol.Biol. (2008)

Release Date

2007-06-26

Peptides

Ornithine carbamoyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ornithine carbamoyltransferase

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