SMTL ID : 6yjb.1

VcaM4I restriction endonuclease 5hmC-ssDNA complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x DC- DA- 5HC- DA- DG: DNA (5'-D(*CP*AP*(5HC)P*AP*G)-3')(Non-covalent)

DC-DA-5HC-DA-DG.1: 29 residues within 4Å: Chain A: S.7, Q.8, K.9, Q.10, T.11, E.15, W.22, S.23, P.24, N.27, K.28, Y.36, F.51, G.54, F.75, W.82, N.125, G.126, N.127, Q.128, A.129, Y.130 Chain B: K.9 Ligands: SO4.4, GOL.18, GOL.22, SO4.23, DC-DA-5HC-DA-DG.24, SO4.46 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.130 Hydrogen bonds: A:Q.10, A:T.11, A:T.11, A:E.15, A:W.82, A:A.129 pi-Stacking: A:W.82 DC-DA-5HC-DA-DG.24: 29 residues within 4Å: Chain A: K.9 Chain B: S.7, Q.8, K.9, Q.10, T.11, E.15, W.22, S.23, P.24, N.27, K.28, Y.36, F.51, G.54, F.75, W.82, N.125, G.126, N.127, Q.128, A.129, Y.130 Ligands: DC-DA-5HC-DA-DG.1, SO4.23, SO4.27, GOL.41, GOL.45, SO4.46 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.130 Hydrogen bonds: B:Q.10, B:T.11, B:E.15, B:Y.36, B:W.82, B:A.129 pi-Stacking: B:W.82

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

SO4.2: 4 residues within 4Å: Chain A: P.44, R.63, S.64, H.65 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: P.135, H.136 Ligand excluded by PLIP SO4.4: 6 residues within 4Å: Chain A: N.27, Q.32, S.33, H.34, Y.35 Ligands: DC-DA-5HC-DA-DG.1 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: H.34, N.37 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: K.25, W.87 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: A.83, N.84, D.85 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: T.164, A.167, R.192 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: S.291, K.292, Q.293 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain A: N.232, N.233, Q.234 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain A: E.184, R.201, L.237 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain B: K.9 Ligands: DC-DA-5HC-DA-DG.1, DC-DA-5HC-DA-DG.1, GOL.22, DC-DA-5HC-DA-DG.24 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain B: P.44, R.63, S.64, H.65 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain B: P.135, H.136 Ligand excluded by PLIP SO4.27: 6 residues within 4Å: Chain B: N.27, Q.32, S.33, H.34, Y.35 Ligands: DC-DA-5HC-DA-DG.24 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain B: H.34, N.37 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain B: K.25, W.87 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain B: A.83, N.84, D.85 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain B: T.164, A.167, R.192 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain B: S.291, K.292, Q.293 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain B: N.232, N.233, Q.234 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain B: E.184, R.201, L.237 Ligand excluded by PLIP SO4.46: 5 residues within 4Å: Chain A: K.9 Ligands: DC-DA-5HC-DA-DG.1, DC-DA-5HC-DA-DG.24, DC-DA-5HC-DA-DG.24, GOL.45 Ligand excluded by PLIP

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 2 residues within 4Å: Chain A: F.16, E.17 Ligand excluded by PLIP GOL.10: 2 residues within 4Å: Chain A: Y.69, N.70 Ligand excluded by PLIP GOL.11: 10 residues within 4Å: Chain A: K.9, Q.10, N.53, A.78 Chain B: K.9, Q.10, A.78 Ligands: GOL.12, GOL.34, GOL.35 Ligand excluded by PLIP GOL.12: 11 residues within 4Å: Chain A: Q.10, T.11, F.12, K.13, Q.14 Chain B: Q.10, K.13, Q.14 Ligands: GOL.11, GOL.34, GOL.35 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain A: K.103, A.104, I.106 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain A: S.148, E.151, F.155, K.271, N.273 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain A: G.156, F.157, T.160, H.251, K.255 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain A: A.78, G.79, A.80, D.81, W.82 Ligands: DC-DA-5HC-DA-DG.1, GOL.22 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain A: Q.10, Q.128 Chain B: K.9 Ligands: DC-DA-5HC-DA-DG.1, DC-DA-5HC-DA-DG.1, DC-DA-5HC-DA-DG.1, GOL.18, SO4.23 Ligand excluded by PLIP GOL.32: 2 residues within 4Å: Chain B: F.16, E.17 Ligand excluded by PLIP GOL.33: 2 residues within 4Å: Chain B: Y.69, N.70 Ligand excluded by PLIP GOL.34: 10 residues within 4Å: Chain A: K.9, Q.10, A.78 Chain B: K.9, Q.10, N.53, A.78 Ligands: GOL.11, GOL.12, GOL.35 Ligand excluded by PLIP GOL.35: 11 residues within 4Å: Chain A: Q.10, K.13, Q.14 Chain B: Q.10, T.11, F.12, K.13, Q.14 Ligands: GOL.11, GOL.12, GOL.34 Ligand excluded by PLIP GOL.36: 3 residues within 4Å: Chain B: K.103, A.104, I.106 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain B: S.148, E.151, F.155, K.271, N.273 Ligand excluded by PLIP GOL.40: 5 residues within 4Å: Chain B: G.156, F.157, T.160, H.251, K.255 Ligand excluded by PLIP GOL.41: 7 residues within 4Å: Chain B: A.78, G.79, A.80, D.81, W.82 Ligands: DC-DA-5HC-DA-DG.24, GOL.45 Ligand excluded by PLIP GOL.45: 8 residues within 4Å: Chain A: K.9 Chain B: Q.10, Q.128 Ligands: DC-DA-5HC-DA-DG.24, DC-DA-5HC-DA-DG.24, DC-DA-5HC-DA-DG.24, GOL.41, SO4.46 Ligand excluded by PLIP

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

CL.15: 2 residues within 4Å: Chain A: Y.67, S.68 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: Q.121, D.122 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain B: Y.67, S.68 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain B: Q.121, D.122 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pastor, M. et al., Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA. Nucleic Acids Res. (2021)

Release Date

2020-12-23

Peptides

HNH endonuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

HNH endonuclease

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