SMTL ID : 6x91.4 (3 other biounits)

Crystal structure of MBP-fused human APOBEC1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.51 Å

Oligo State

homo-dimer

Ligands

4 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 14 residues within 4Å: Chain A: N.13, D.15, K.16, W.63, A.64, D.66, R.67, E.112, E.154, P.155, Y.156, W.231, W.341, R.345 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.66, A:R.67, A:R.67, A:Y.156, A:R.345 GLC-GLC.2: 10 residues within 4Å: Chain A: G.75, L.77, A.78, A.269, K.274, R.390, K.391, R.555, A.556, Q.557 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.77, A:R.390, A:K.391, A:K.391 GLC-GLC.3: 11 residues within 4Å: Chain B: N.13, W.63, A.64, D.66, R.67, E.112, Y.156, W.231, G.261, M.331, W.341 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.13, B:W.63, B:A.64, B:E.112 GLC-GLC.4: 9 residues within 4Å: Chain B: G.75, A.78, E.79, A.269, K.274, L.389, R.390, A.556, Q.557 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.79, B:K.274, B:K.274, B:R.390, B:A.556

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: H.418, C.450, C.453 Ligands: CAC.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.418, A:C.450, A:C.453 ZN.7: 4 residues within 4Å: Chain B: H.418, C.450, C.453 Ligands: CAC.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.418, B:C.450, B:C.453

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.6: 8 residues within 4Å: Chain A: H.418, W.447, S.448, P.449, C.450, C.453, F.477 Ligands: ZN.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.450 CAC.8: 8 residues within 4Å: Chain B: H.418, W.447, S.448, P.449, C.450, C.453, F.477 Ligands: ZN.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wolfe, A.D. et al., The structure of APOBEC1 and insights into its RNA and DNA substrate selectivity. NAR Cancer (2020)

Release Date

2020-12-09

Peptides

Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera

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