SMTL ID : 7edb.1

EcoT38I restriction endonuclease complexed with DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.231, E.245, V.246 Chain D: C.10 Ligands: CA.19 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.231, A:E.245, A:V.246, H2O.5, H2O.12 CA.2: 1 residues within 4Å: Chain A: D.122 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.122 CA.10: 3 residues within 4Å: Chain B: N.172, S.173, N.175 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.173, H2O.7, H2O.9, H2O.10 CA.19: 4 residues within 4Å: Chain A: D.231 Chain D: T.9, C.10 Ligands: CA.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.231, H2O.1, H2O.3, H2O.3, H2O.4

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 9 residues within 4Å: Chain A: T.43, R.126, D.130, D.191, S.340 Chain C: A.6, G.7 Chain D: G.12, C.13 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.43, A:R.126, A:D.130, A:D.191, A:S.340, A:S.340 TRS.4: 6 residues within 4Å: Chain A: K.58, P.62, R.63, V.64, N.65, D.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.62, A:N.65, A:D.76 TRS.13: 6 residues within 4Å: Chain B: K.58, P.62, R.63, V.64, N.65, D.76 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.58, B:P.62, B:N.65, B:D.76 TRS.14: 6 residues within 4Å: Chain B: T.43, H.44, R.126, D.130 Chain C: C.12, G.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.43, B:R.126, B:D.130 Water bridges: B:L.45

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: D.177 Chain B: A.294, G.297, S.299 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.297 GOL.6: 2 residues within 4Å: Chain A: T.29, E.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.152 GOL.7: 2 residues within 4Å: Chain A: A.59, Y.151 No protein-ligand interaction detected (PLIP) GOL.8: 3 residues within 4Å: Chain A: N.31, W.33, V.34 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.33 GOL.15: 2 residues within 4Å: Chain B: N.31, Q.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.31 GOL.16: 2 residues within 4Å: Chain B: A.59, T.148 No protein-ligand interaction detected (PLIP) GOL.17: 3 residues within 4Å: Chain B: T.29, N.30, E.152 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.30 Water bridges: B:N.30 GOL.18: 1 residues within 4Å: Chain C: G.2 No protein-ligand interaction detected (PLIP)

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

CL.9: 3 residues within 4Å: Chain A: K.101, R.164, T.165 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain B: R.126 Chain C: A.11, C.12 Chain D: G.3, T.4, G.5 Ligand excluded by PLIP

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

NA.11: 3 residues within 4Å: Chain B: V.219, D.231, E.245 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.231, B:K.247

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.12: 3 residues within 4Å: Chain B: E.8, Y.11, K.92 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kita, K. et al., Structural analysis of EcoT38I restriction endonuclease. To Be Published

Release Date

2022-03-16

Peptides

EcoT38I restriction endonuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

EcoT38I restriction endonuclease

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