SMTL ID : 6pqn.1

Crystal structure of HzTransib transposase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.224, C.227, H.392, H.397 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.224, A:C.227, A:H.392, A:H.397 ZN.12: 5 residues within 4Å: Chain B: C.224, C.227, H.392, I.396, H.397 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.224, B:C.227, B:H.392, B:H.397

10 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 7 residues within 4Å: Chain A: D.109, G.110, D.208, K.210, S.255, L.257, H.258 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.109, A:D.208, A:S.255 Salt bridges: A:K.210, A:H.258 PO4.3: 4 residues within 4Å: Chain A: K.278, S.280, G.283, H.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.283 Salt bridges: A:K.278, A:H.286 PO4.4: 2 residues within 4Å: Chain A: Y.386, M.387 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.387 PO4.5: 5 residues within 4Å: Chain A: H.269, Y.272, R.273, L.290, K.294 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.294, A:D.310 Salt bridges: A:H.269, A:R.273, A:K.294 PO4.6: 4 residues within 4Å: Chain A: R.273, S.280, A.281, R.282 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.280, A:A.281 Salt bridges: A:R.273, A:R.282 PO4.13: 2 residues within 4Å: Chain B: H.431, H.432 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.431, B:H.432 PO4.14: 4 residues within 4Å: Chain B: R.348, E.369, Y.370, T.373 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.348 PO4.15: 7 residues within 4Å: Chain B: R.260, R.326, Q.354, T.357, H.467, T.471, Y.472 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.354, B:T.357, B:T.471, B:Y.472 Salt bridges: B:R.260, B:H.467 PO4.16: 4 residues within 4Å: Chain B: H.269, Y.272, R.273, K.294 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:H.269, B:R.273, B:K.294 PO4.17: 6 residues within 4Å: Chain B: D.208, G.253, L.254, S.255, H.258, K.393 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.255 Salt bridges: B:K.393

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: R.260, R.326, Q.354, T.357, H.467, T.471, Y.472 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.260, A:Q.354, A:T.357, A:T.471, A:Y.472 GOL.8: 5 residues within 4Å: Chain A: R.469, Q.470, T.471, Y.472, K.474 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.469 Water bridges: A:R.469 GOL.9: 6 residues within 4Å: Chain A: C.154, E.360, I.361, I.362, I.402, N.405 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.154, A:I.362, A:I.362 GOL.10: 2 residues within 4Å: Chain A: H.432 Chain B: K.334 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.334 GOL.18: 3 residues within 4Å: Chain B: H.432, S.433, K.436 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.433, B:K.436, B:K.436

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 3 residues within 4Å: Chain B: E.416, D.465, H.467 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., Structures of a RAG-like transposase during cut-and-paste transposition. Nature (2019)

Release Date

2019-10-09

Peptides

Putative DNA-mediated transposase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative DNA-mediated transposase

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