SMTL ID : 3d6n.1 (1 other biounit)

Crystal Structure of Aquifex Dihydroorotase Activated by Aspartate Transcarbamoylase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-6-6-mer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.61, H.63, D.153, D.305 Ligands: FLC.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.61, A:H.63, A:D.153, A:D.153, A:D.305 ZN.4: 5 residues within 4Å: Chain C: H.61, H.63, D.153, D.305 Ligands: FLC.5 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.61, C:H.63, C:D.153, C:D.153, C:D.305 ZN.7: 5 residues within 4Å: Chain E: H.61, H.63, D.153, D.305 Ligands: FLC.8 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:H.61, E:H.63, E:D.153, E:D.153, E:D.305 ZN.10: 5 residues within 4Å: Chain G: H.61, H.63, D.153, D.305 Ligands: FLC.11 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:H.61, G:H.63, G:D.153, G:D.153, G:D.305 ZN.13: 5 residues within 4Å: Chain I: H.61, H.63, D.153, D.305 Ligands: FLC.14 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:H.61, I:H.63, I:D.153, I:D.153, I:D.305 ZN.16: 5 residues within 4Å: Chain K: H.61, H.63, D.153, D.305 Ligands: FLC.17 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:H.61, K:H.63, K:D.153, K:D.153, K:D.305

12 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 16 residues within 4Å: Chain A: H.61, H.63, R.65, N.95, D.153, G.154, H.180, H.232, V.277, N.278, D.305, A.307, H.309, P.322, G.323 Ligands: ZN.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.307 Hydrogen bonds: A:N.95, A:N.278, A:P.322, A:P.322 Water bridges: A:G.154, A:N.278, A:I.324 Salt bridges: A:H.61, A:H.63, A:H.63, A:R.65, A:H.180, A:H.232, A:H.309 FLC.3: 7 residues within 4Å: Chain B: T.48, R.97, H.126, R.159, V.160, R.213, G.251 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.160 Hydrogen bonds: B:R.97 Water bridges: B:R.159, B:R.159, B:R.213 Salt bridges: B:R.97, B:R.97, B:H.126, B:H.126, B:R.159 FLC.5: 16 residues within 4Å: Chain C: H.61, H.63, R.65, N.95, D.153, G.154, H.180, H.232, V.277, N.278, D.305, A.307, H.309, P.322, G.323 Ligands: ZN.4 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:A.307 Hydrogen bonds: C:N.95, C:N.278, C:P.322, C:P.322 Water bridges: C:G.154, C:N.278, C:I.324 Salt bridges: C:H.61, C:H.63, C:H.63, C:R.65, C:H.180, C:H.232, C:H.309 FLC.6: 7 residues within 4Å: Chain D: T.48, R.97, H.126, R.159, V.160, R.213, G.251 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:V.160 Hydrogen bonds: D:R.97 Water bridges: D:R.159, D:R.159, D:R.213 Salt bridges: D:R.97, D:R.97, D:H.126, D:H.126, D:R.159 FLC.8: 16 residues within 4Å: Chain E: H.61, H.63, R.65, N.95, D.153, G.154, H.180, H.232, V.277, N.278, D.305, A.307, H.309, P.322, G.323 Ligands: ZN.7 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:A.307 Hydrogen bonds: E:N.95, E:N.278, E:P.322, E:P.322 Water bridges: E:G.154, E:N.278, E:I.324 Salt bridges: E:H.61, E:H.63, E:H.63, E:R.65, E:H.180, E:H.232, E:H.309 FLC.9: 7 residues within 4Å: Chain F: T.48, R.97, H.126, R.159, V.160, R.213, G.251 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:V.160 Hydrogen bonds: F:R.97 Water bridges: F:R.159, F:R.159, F:R.213 Salt bridges: F:R.97, F:R.97, F:H.126, F:H.126, F:R.159 FLC.11: 16 residues within 4Å: Chain G: H.61, H.63, R.65, N.95, D.153, G.154, H.180, H.232, V.277, N.278, D.305, A.307, H.309, P.322, G.323 Ligands: ZN.10 15 PLIP interactions: 15 interactions with chain G Hydrophobic interactions: G:A.307 Hydrogen bonds: G:N.95, G:N.278, G:P.322, G:P.322 Water bridges: G:G.154, G:N.278, G:I.324 Salt bridges: G:H.61, G:H.63, G:H.63, G:R.65, G:H.180, G:H.232, G:H.309 FLC.12: 7 residues within 4Å: Chain H: T.48, R.97, H.126, R.159, V.160, R.213, G.251 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:V.160 Hydrogen bonds: H:T.48, H:R.97 Water bridges: H:R.159, H:R.159, H:R.213 Salt bridges: H:R.97, H:R.97, H:H.126, H:H.126, H:R.159 FLC.14: 16 residues within 4Å: Chain I: H.61, H.63, R.65, N.95, D.153, G.154, H.180, H.232, V.277, N.278, D.305, A.307, H.309, P.322, G.323 Ligands: ZN.13 15 PLIP interactions: 15 interactions with chain I Hydrophobic interactions: I:A.307 Hydrogen bonds: I:N.95, I:N.278, I:P.322, I:P.322 Water bridges: I:G.154, I:N.278, I:I.324 Salt bridges: I:H.61, I:H.63, I:H.63, I:R.65, I:H.180, I:H.232, I:H.309 FLC.15: 7 residues within 4Å: Chain J: T.48, R.97, H.126, R.159, V.160, R.213, G.251 11 PLIP interactions: 11 interactions with chain J Hydrophobic interactions: J:V.160 Hydrogen bonds: J:T.48, J:R.97 Water bridges: J:R.159, J:R.159, J:R.213 Salt bridges: J:R.97, J:R.97, J:H.126, J:H.126, J:R.159 FLC.17: 16 residues within 4Å: Chain K: H.61, H.63, R.65, N.95, D.153, G.154, H.180, H.232, V.277, N.278, D.305, A.307, H.309, P.322, G.323 Ligands: ZN.16 15 PLIP interactions: 15 interactions with chain K Hydrophobic interactions: K:A.307 Hydrogen bonds: K:N.95, K:N.278, K:P.322, K:P.322 Water bridges: K:G.154, K:N.278, K:I.324 Salt bridges: K:H.61, K:H.63, K:H.63, K:R.65, K:H.180, K:H.232, K:H.309 FLC.18: 7 residues within 4Å: Chain L: T.48, R.97, H.126, R.159, V.160, R.213, G.251 11 PLIP interactions: 11 interactions with chain L Hydrophobic interactions: L:V.160 Hydrogen bonds: L:T.48, L:R.97 Water bridges: L:R.159, L:R.159, L:R.213 Salt bridges: L:R.97, L:R.97, L:H.126, L:H.126, L:R.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, P. et al., Dihydroorotase from the hyperthermophile Aquifiex aeolicus is activated by stoichiometric association with aspartate transcarbamoylase and forms a one-pot reactor for pyrimidine biosynthesis. Biochemistry (2009)

Release Date

2009-01-20

Peptides

Dihydroorotase: ACEGIK
Aspartate carbamoyltransferase: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

I
A

K
A

B
B

D
B

F
B

H
B

J
B

L
B

Dihydroorotase

Aspartate carbamoyltransferase

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