SMTL ID : 5w1c.1

Crystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with cytidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.18 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.424, C.455, C.458 Ligands: CTN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.424, A:C.455, A:C.458, H2O.1 ZN.4: 4 residues within 4Å: Chain D: H.424, C.455, C.458 Ligands: CTN.5 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.424, D:C.455, D:C.458, H2O.1

2 x CTN: 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE(Covalent)(Non-covalent)

CTN.2: 10 residues within 4Å: Chain A: R.393, T.395, N.419, H.424, W.452, S.453, P.454, C.455, Y.482 Ligands: ZN.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.395, A:T.395, A:T.395, A:N.419, A:S.453, A:C.455, A:Y.482 pi-Stacking: A:H.424, A:Y.482 CTN.5: 9 residues within 4Å: Chain D: R.393, T.395, N.419, H.424, S.453, P.454, C.455, Y.482 Ligands: ZN.4 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:R.393, D:R.393, D:T.395, D:N.419, D:N.419, D:W.452, D:C.455, D:Y.482 pi-Stacking: D:H.424, D:Y.482

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: T.367, N.368, A.370, D.413 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.367, A:N.368 CA.6: 5 residues within 4Å: Chain D: T.367, N.368, A.370, D.413, F.414 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.367, D:N.368, D:D.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiao, Q. et al., AID Recognizes Structured DNA for Class Switch Recombination. Mol. Cell (2017)

Release Date

2017-08-16

Peptides

MBP fused activation-induced cytidine deaminase: AD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
A

MBP fused activation-induced cytidine deaminase