SMTL ID : 2vtb.1 (2 other biounits)

Structure of cryptochrome 3 - DNA complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

hetero-1-1-mer

Ligands

2 x DT- DT- TCP- DT- DT: 5'-D(*DT*DT*DT*DT*DTP)-3'(Non-covalent)

DT-DT-TCP-DT-DT.1: 26 residues within 4Å: Chain A: V.194, Y.195, T.196, R.277, N.278, W.322, F.325, E.326, W.329, N.392, R.393, Q.396, N.432, Y.435, P.443, E.445, D.446, R.447, Y.448, F.449, S.450, K.453, Q.454, Y.458, H.497 Ligands: FAD.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.435 Hydrogen bonds: A:R.277, A:R.277, A:N.278, A:N.392, A:N.392, A:R.393, A:R.393, A:Q.396 DT-DT-TCP-DT-DT.2: 23 residues within 4Å: Chain B: V.194, Y.195, T.196, R.277, N.278, W.322, F.325, E.326, W.329, N.392, R.393, Q.396, N.432, Y.435, R.446, Y.447, F.448, S.449, K.452, Q.453, Y.457, H.496 Ligands: FAD.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.435 Hydrogen bonds: B:R.277, B:R.277, B:N.278, B:N.392, B:N.392, B:R.393, B:R.393, B:Q.396

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.3: 27 residues within 4Å: Chain A: Y.273, S.286, T.287, K.288, F.289, S.290, L.293, E.326, L.327, R.330, F.333, F.389, M.390, N.392, R.395, Q.396, F.417, L.421, D.423, Y.424, D.425, S.428, N.429, N.432, W.433 Ligands: DT-DT-TCP-DT-DT.1, DT-DT-TCP-DT-DT.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:R.395, A:Q.396, A:F.417, A:F.417, A:N.432 Hydrogen bonds: A:Y.273, A:Y.273, A:T.287, A:T.287, A:K.288, A:F.289, A:S.290, A:S.290, A:N.392, A:R.395, A:D.423, A:D.425, A:N.432, A:N.432 Water bridges: A:S.286, A:S.286, A:S.286, A:S.290, A:N.392, A:S.428, A:S.428 pi-Cation interactions: A:R.395 FAD.6: 27 residues within 4Å: Chain B: Y.273, S.286, T.287, K.288, F.289, S.290, L.293, E.326, L.327, R.330, F.333, F.389, M.390, N.392, R.395, Q.396, F.417, L.421, D.423, Y.424, D.425, S.428, N.429, N.432, W.433 Ligands: DT-DT-TCP-DT-DT.2, DT-DT-TCP-DT-DT.2 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:R.395, B:Q.396, B:F.417, B:F.417, B:N.432 Hydrogen bonds: B:Y.273, B:T.287, B:K.288, B:F.289, B:S.290, B:S.290, B:E.326, B:N.392, B:R.395, B:D.423, B:D.423, B:D.425, B:N.432, B:N.432 Water bridges: B:Y.285, B:S.286, B:S.286, B:N.392, B:S.428, B:S.428 pi-Cation interactions: B:R.395

2 x MHF: 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID(Non-covalent)

MHF.4: 17 residues within 4Å: Chain A: H.84, K.90, C.147, S.148, E.149, E.150, N.342, F.345, H.346, E.418, Y.424, P.426, Y.430 Chain B: F.189, D.190, D.193, K.339 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.345 Hydrogen bonds: A:K.90, A:E.149, A:N.342, A:E.418, A:Y.424, A:Y.424, A:Y.424, B:D.190, B:D.190 Water bridges: A:H.84, A:E.149, B:K.339 Salt bridges: A:E.149, A:E.150, A:H.346, A:E.418, B:K.339 MHF.7: 17 residues within 4Å: Chain A: F.189, D.190, D.193, K.339 Chain B: H.84, K.90, C.147, S.148, E.149, E.150, N.342, F.345, H.346, E.418, Y.424, P.426, Y.430 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:N.342, B:F.345 Hydrogen bonds: B:K.90, B:E.149, B:N.342, B:E.418, B:Y.424, B:Y.424, A:D.190, A:D.190 Water bridges: B:E.149, B:E.149, A:L.191, A:K.339 Salt bridges: B:E.149, B:E.150, B:H.346, B:E.418, A:K.339

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

CL.5: 5 residues within 4Å: Chain A: R.52, D.55, D.57, H.143, R.301 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: R.52, D.55, D.57, H.143, R.301 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain B: G.282 Ligand excluded by PLIP

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

ACT.10: 5 residues within 4Å: Chain B: R.120, F.135, V.224, D.225, D.226 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.135, B:D.225 Hydrogen bonds: B:D.225, B:D.226 Salt bridges: B:R.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pokorny, R. et al., Recognition and Repair of Uv Lesions in Loop Structures of Duplex DNA by Dash-Type Cryptochrome. Proc.Natl.Acad.Sci.USA (2008)

Release Date

2009-06-02

Peptides

CRYPTOCHROME DASH: A
CRYPTOCHROME DASH: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CRYPTOCHROME DASH

CRYPTOCHROME DASH

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