SMTL ID : 5jk0.1

Crystal structure of XerH site-specific recombinase bound to difH substrate: pre-cleavage complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 1 residues within 4Å: Chain A: Q.57 No protein-ligand interaction detected (PLIP) GOL.2: 3 residues within 4Å: Chain A: F.226, Y.233, L.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.226, A:L.228 GOL.5: 3 residues within 4Å: Chain B: D.141, I.153 Chain D: K.142 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Water bridges: B:K.142, B:N.155, B:I.156, D:D.141 GOL.6: 9 residues within 4Å: Chain B: T.29, S.30, L.31, S.32, N.33 Chain C: L.114, S.115, T.118, K.126 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:T.118, C:T.118, B:T.29, B:N.33 Water bridges: C:S.115, C:S.115, C:K.126, B:S.32 GOL.7: 4 residues within 4Å: Chain B: K.196, L.267, Y.268, Q.279 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.268, B:Q.279 Water bridges: B:E.264

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: Y.86, F.87, K.89, R.91, F.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.86 EDO.8: 4 residues within 4Å: Chain B: Q.39, N.40 Chain C: K.89, Y.117 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:K.89, B:Q.39, B:N.40 EDO.10: 4 residues within 4Å: Chain A: N.155 Chain C: Y.26, Y.139, Q.143 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.143, A:N.155 EDO.11: 7 residues within 4Å: Chain C: N.74, T.75, L.78, P.79, N.128, Y.129 Chain F: A.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.75 Water bridges: C:N.128 EDO.12: 3 residues within 4Å: Chain D: L.81, K.82, E.85 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.55, D:S.55 Water bridges: D:E.85

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

CL.4: 4 residues within 4Å: Chain A: H.325, L.327 Chain C: H.325, L.327 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 6 residues within 4Å: Chain B: H.4, R.22, R.25, L.49, N.50, Q.51 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.4, B:R.22, B:R.25, B:R.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bebel, A. et al., Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending. Elife (2016)

Release Date

2016-12-28

Peptides

Tyrosine recombinase XerH: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Tyrosine recombinase XerH

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