SMTL ID : 5cr4.1

Crystal structure of the Sleeping Beauty transposase catalytic domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

25 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: R.56, Y.57, R.183 Chain B: K.200 Ligand excluded by PLIP SO4.2: 1 residues within 4Å: Chain A: K.229 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: H.97, K.98, H.191, Q.195 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: H.17, K.19, A.20 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: R.16, Q.161 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: R.178, K.200 Chain B: Y.57, K.67 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: L.187, T.188, H.191 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: T.118, R.121 Ligand excluded by PLIP SO4.9: 7 residues within 4Å: Chain A: D.134, N.135, D.136, W.158, S.160, Q.161 Ligands: GOL.17 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: T.34, R.37, N.38 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: R.60, G.63 Chain B: K.122 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: Q.14, R.16 Ligand excluded by PLIP SO4.13: 1 residues within 4Å: Chain A: R.127 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain B: H.97, K.98, H.191, Q.195 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain A: K.200 Chain B: R.56, Y.57, R.183 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain B: W.59, P.68, K.69, N.70 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain B: D.134, N.135, D.136, S.160, Q.161 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain B: R.16, Q.161 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain A: Y.57 Chain B: R.178, K.200, H.202 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain B: T.188, H.191 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain B: S.141, K.142 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: K.215, K.229, Y.230 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain B: T.34, R.37, N.38 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain B: R.60, K.61, K.62, G.63 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain B: H.202, N.204 Ligand excluded by PLIP

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 2 residues within 4Å: Chain A: G.51, H.52 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.52, A:R.180 Water bridges: A:G.51, A:H.52, A:R.180 GOL.15: 3 residues within 4Å: Chain A: K.113, W.147, N.151 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.113, A:N.151, A:N.151 Water bridges: A:D.150, A:D.150, A:D.150 GOL.16: 2 residues within 4Å: Chain A: R.121, K.122 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.121, A:R.121, A:K.122 GOL.17: 9 residues within 4Å: Chain A: D.43, Q.132, D.134, W.158, S.162, P.163, N.166, E.169 Ligands: SO4.9 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.132, A:D.134, A:S.162, A:S.162, A:N.166 Water bridges: A:S.42, A:D.43 GOL.18: 1 residues within 4Å: Chain A: R.183 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.183, A:R.183 Water bridges: A:D.54, A:R.183 GOL.32: 6 residues within 4Å: Chain B: H.17, K.18, K.19, A.20, R.23 Ligands: GOL.37 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.17, B:K.19, B:A.20, B:R.23, B:R.23 Water bridges: B:S.160 GOL.33: 4 residues within 4Å: Chain B: D.104, A.105, V.106, K.138 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.105, B:V.106 GOL.34: 5 residues within 4Å: Chain B: K.46, E.48, K.76, G.80, S.81 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.48, B:K.76, B:G.80, B:S.81 Water bridges: B:G.80 GOL.35: 4 residues within 4Å: Chain B: L.22, K.221, Q.222, K.224 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.222 GOL.36: 2 residues within 4Å: Chain B: R.180, R.183 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.180, B:R.180, B:R.183, B:R.183 Water bridges: B:H.55 GOL.37: 6 residues within 4Å: Chain B: N.15, R.16, H.17, K.18, K.19 Ligands: GOL.32 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.16, B:H.17, B:K.18, B:K.19

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.31: 7 residues within 4Å: Chain B: H.28, F.35, V.130, K.154, V.155, L.156, E.157 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.157 Water bridges: B:V.155 Salt bridges: B:H.28, B:K.31

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.38: 7 residues within 4Å: Chain B: K.46, I.47, E.48, H.52, N.53, K.176, R.180 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.48, B:H.52, B:N.53, B:N.53 Salt bridges: B:E.48, B:R.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Voigt, F. et al., Sleeping Beauty transposase structure allows rational design of hyperactive variants for genetic engineering. Nat Commun (2016)

Release Date

2016-03-30

Peptides

Sleeping Beauty transposase, SB100X: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sleeping Beauty transposase, SB100X