SMTL ID : 1q8f.1

Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.11, D.16, N.40, V.124, D.240 Ligands: GOL.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.11, A:D.16, A:V.124, A:D.240, H2O.1 CA.7: 6 residues within 4Å: Chain B: D.11, D.16, N.40, V.124, D.240 Ligands: GOL.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.16, B:D.16, B:V.124, B:D.240, H2O.12 CA.11: 6 residues within 4Å: Chain C: D.11, D.16, N.40, V.124, D.240 Ligands: GOL.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.11, C:D.16, C:V.124, C:D.240, H2O.19 CA.16: 6 residues within 4Å: Chain D: D.11, D.16, N.40, V.124, D.240 Ligands: GOL.17 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.11, D:D.16, D:V.124, D:D.240, H2O.29

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: D.15, V.124, M.150, N.158, E.164, F.165, N.166, H.239, D.240 Ligands: CA.1, GOL.3 Ligand excluded by PLIP GOL.3: 9 residues within 4Å: Chain A: N.40, A.78, I.81, H.82, N.158, F.159, F.165, Y.231 Ligands: GOL.2 Ligand excluded by PLIP GOL.4: 3 residues within 4Å: Chain A: Q.74 Chain B: R.135 Ligands: GOL.6 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: M.134, R.135, V.176, T.179, S.180 Ligands: GOL.10 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: Q.69, P.70, R.73, Q.74, Q.75 Chain B: R.135 Ligands: GOL.4 Ligand excluded by PLIP GOL.8: 11 residues within 4Å: Chain B: D.15, V.124, M.150, N.158, E.164, F.165, N.166, H.239, D.240 Ligands: CA.7, GOL.9 Ligand excluded by PLIP GOL.9: 9 residues within 4Å: Chain B: N.40, A.78, I.81, H.82, N.158, F.159, F.165, Y.231 Ligands: GOL.8 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: R.135 Chain B: Q.69, P.70, R.73, Q.74, Q.75 Ligands: GOL.5 Ligand excluded by PLIP GOL.12: 11 residues within 4Å: Chain C: D.15, V.124, M.150, N.158, E.164, F.165, N.166, H.239, D.240 Ligands: CA.11, GOL.13 Ligand excluded by PLIP GOL.13: 9 residues within 4Å: Chain C: N.40, A.78, I.81, H.82, N.158, F.159, F.165, Y.231 Ligands: GOL.12 Ligand excluded by PLIP GOL.14: 8 residues within 4Å: Chain C: M.134, R.135, L.141, V.176, T.179, S.180 Chain D: Q.74 Ligands: GOL.19 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain C: Q.69, P.70, R.73, Q.74, Q.75 Chain D: R.135 Ligands: GOL.20 Ligand excluded by PLIP GOL.17: 11 residues within 4Å: Chain D: D.15, V.124, M.150, N.158, E.164, F.165, N.166, H.239, D.240 Ligands: CA.16, GOL.18 Ligand excluded by PLIP GOL.18: 9 residues within 4Å: Chain D: N.40, A.78, I.81, H.82, N.158, F.159, F.165, Y.231 Ligands: GOL.17 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain C: R.135 Chain D: Q.69, P.70, R.73, Q.74, Q.75 Ligands: GOL.14 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain D: M.134, R.135, V.176, T.179, S.180 Ligands: GOL.15 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giabbai, B. et al., Crystal structure to 1.7 a of the Escherichia coli pyrimidine nucleoside hydrolase YeiK, a novel candidate for cancer gene therapy. STRUCTURE (2004)

Release Date

2004-05-11

Peptides

Pyrimidine nucleoside hydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyrimidine nucleoside hydrolase