SMTL ID : 4lam.1

Crystal structure of Cordyceps militaris IDCase D323N mutant in complex with 5-carboxyl-uracil

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.12, H.14, H.195, N.323 Ligands: 5CU.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.12, A:H.14, A:H.195 ZN.6: 5 residues within 4Å: Chain B: H.12, H.14, H.195, N.323 Ligands: 5CU.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.12, B:H.14, B:H.195

2 x 5CU: 2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid(Non-covalent)

5CU.2: 14 residues within 4Å: Chain A: H.12, H.14, L.46, R.68, N.98, H.195, L.218, F.222, H.251, N.323, F.326, F.327 Chain B: R.262 Ligands: ZN.1 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.222 Hydrogen bonds: A:R.68, A:R.68, A:N.98, A:N.98, A:N.323 Salt bridges: A:H.12, A:H.195, A:H.251, B:R.262 pi-Stacking: A:F.326 Water bridges: B:R.262, B:R.262 5CU.7: 14 residues within 4Å: Chain A: R.262 Chain B: H.12, H.14, L.46, R.68, N.98, H.195, L.218, F.222, H.251, N.323, F.326, F.327 Ligands: ZN.6 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.222 Hydrogen bonds: B:R.68, B:R.68, B:N.98, B:N.98, B:N.323 Salt bridges: B:H.12, B:H.195, B:H.251, A:R.262 pi-Stacking: B:F.326 Water bridges: A:R.262, A:R.262

4 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.3: 8 residues within 4Å: Chain A: Y.234, M.235, G.237, D.240, K.278, R.283 Chain B: E.211, Y.212 No protein-ligand interaction detected (PLIP) P6G.4: 7 residues within 4Å: Chain A: D.102, L.139, S.140, S.167, L.169, G.170, Y.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.167, A:Y.198 P6G.5: 4 residues within 4Å: Chain A: D.114, A.148, E.151, R.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.152 Water bridges: A:A.115 P6G.8: 8 residues within 4Å: Chain A: E.211, Y.212 Chain B: Y.234, M.235, G.237, D.240, K.278, R.283 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, S. et al., Crystal structures of isoorotate decarboxylases reveal a novel catalytic mechanism of 5-carboxyl-uracil decarboxylation and shed light on the search for DNA decarboxylase. Cell Res. (2013)

Release Date

2013-10-02

Peptides

Uracil-5-carboxylate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uracil-5-carboxylate decarboxylase

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