SMTL ID : 5jfy.2 (1 other biounit)

Crystal structure of a plant cytidine deaminase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: F.39, N.55, H.66, A.67 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: F.39, N.55, H.66, A.67, E.68 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.66, C.96, M.98, C.99 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.66, A:C.96, A:C.99 ZN.8: 4 residues within 4Å: Chain B: H.66, C.96, M.98, C.99 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.66, B:C.96, B:C.99, H2O.3

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: V.24, A.27, P.38, F.39, G.40, S.92, C.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.92, A:S.92 GOL.4: 3 residues within 4Å: Chain A: L.13, D.14, S.15 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.14, A:D.14, A:D.14, A:S.15, A:S.15 GOL.5: 8 residues within 4Å: Chain A: C.93, E.94, Y.113, G.114, A.115, K.116, A.117, E.118 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.94, A:E.94, A:E.94, A:K.116 Water bridges: A:A.117

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 4 residues within 4Å: Chain A: G.34, D.35, L.58, K.59 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.58 Salt bridges: A:K.59

1 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.9: 8 residues within 4Å: Chain A: I.82 Chain B: G.36, G.37, P.38, F.39, N.55, V.57, L.58 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.58 Hydrogen bonds: B:G.37 Water bridges: B:N.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taylor, M.W. et al., To be published. To Be Published

Release Date

2017-04-26

Peptides

Deoxycytidine deaminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Deoxycytidine deaminase

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