SMTL ID : 3ksk.1 (2 other biounits)

Crystal Structure of single chain PvuII

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: T.45, Y.66, I.99, R.113, I.155 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.60, A:Y.66 Salt bridges: A:R.113 SO4.2: 4 residues within 4Å: Chain A: I.233, K.237, R.264 Chain B: H.162 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Water bridges: B:K.24, B:K.24, B:H.25, A:R.264 Salt bridges: B:K.24, B:H.162, A:K.237, A:R.264 SO4.4: 4 residues within 4Å: Chain B: L.8, W.12, Q.200, Y.316 2 PLIP interactions: 2 interactions with chain B Water bridges: B:I.268, B:Y.316 SO4.5: 4 residues within 4Å: Chain B: T.205, L.207, R.273, I.315 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.205 Salt bridges: B:R.273 SO4.6: 4 residues within 4Å: Chain B: N.194, I.231, N.232, T.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.194, B:N.232, B:N.232, B:T.236 SO4.9: 5 residues within 4Å: Chain C: T.45, Y.66, I.99, R.113, I.155 3 PLIP interactions: 3 interactions with chain C Water bridges: C:D.60, C:Y.66 Salt bridges: C:R.113 SO4.10: 4 residues within 4Å: Chain C: I.233, K.237, R.264 Chain D: H.162 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Water bridges: C:R.264, D:K.24, D:K.24, D:H.25 Salt bridges: C:K.237, C:R.264, D:K.24, D:H.162 SO4.12: 4 residues within 4Å: Chain D: L.8, W.12, Q.200, Y.316 2 PLIP interactions: 2 interactions with chain D Water bridges: D:I.268, D:Y.316 SO4.13: 4 residues within 4Å: Chain D: T.205, L.207, R.273, I.315 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.205 Salt bridges: D:R.273 SO4.14: 4 residues within 4Å: Chain D: N.194, I.231, N.232, T.236 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.194, D:N.232, D:N.232, D:T.236

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 8 residues within 4Å: Chain A: I.44, I.108, E.109, A.110, I.111, K.154, I.155, G.157 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.108, A:A.110, A:I.111, A:K.154 Hydrogen bonds: A:I.111, A:I.155, A:I.155, A:G.157 MPD.11: 8 residues within 4Å: Chain C: I.44, I.108, E.109, A.110, I.111, K.154, I.155, G.157 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.108, C:A.110, C:I.111, C:K.154 Hydrogen bonds: C:I.111, C:I.155, C:I.155, C:G.157

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

TRS.7: 9 residues within 4Å: Chain B: I.44, I.108, E.109, A.110, I.111, K.154, I.155, Y.156, G.157 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.108, B:I.111, B:G.157 TRS.8: 5 residues within 4Å: Chain B: Q.40, I.108, L.168, L.169, W.172 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.40 TRS.15: 9 residues within 4Å: Chain D: I.44, I.108, E.109, A.110, I.111, K.154, I.155, Y.156, G.157 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.108, D:I.111, D:G.157 TRS.16: 5 residues within 4Å: Chain D: Q.40, I.108, L.168, L.169, W.172 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meramveliotaki, C. et al., Crystal Structure of single chain PvuII. To be Published

Release Date

2010-04-14

Peptides

Type-2 restriction enzyme PvuII: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Type-2 restriction enzyme PvuII

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