SMTL ID : 3oq2.3 (2 other biounits)

Structure of a CRISPR associated protein Cas2 from Desulfovibrio vulgaris

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: F.18, Q.24, L.27, Y.43 Chain D: Y.43 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Y.43, A:Y.43, D:Y.43 NA.9: 5 residues within 4Å: Chain B: F.18, Q.24, L.27, Y.43 Chain C: Y.43 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Y.43, B:F.18, B:Y.43

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

TRS.2: 7 residues within 4Å: Chain A: S.17, D.20, P.21, G.22, G.23, R.26, K.70 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.17, A:S.17, A:G.22, A:G.23, A:R.26, A:R.26, A:K.70 Water bridges: A:S.17 TRS.10: 7 residues within 4Å: Chain B: S.17, D.20, P.21, G.22, G.23, R.26, K.70 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.17, B:S.17, B:G.22, B:G.23, B:R.26, B:R.26, B:K.70 Water bridges: B:S.17

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

CL.3: 1 residues within 4Å: Chain A: E.19 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: E.19 Ligand excluded by PLIP

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

SO4.4: 3 residues within 4Å: Chain A: K.57, R.61 Chain C: Q.35 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Water bridges: A:K.57, A:K.57, A:H.60, A:H.60, A:R.61, A:R.61 Salt bridges: A:K.57, A:R.61 Hydrogen bonds: C:Q.35 SO4.5: 7 residues within 4Å: Chain A: L.27, R.28, A.31, R.40, Y.43 Chain D: Q.24, R.28 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Y.43, D:R.28 Water bridges: A:R.28, A:R.28, A:R.40, A:R.40, A:R.40, A:R.40, A:Y.43 Salt bridges: A:R.40 SO4.6: 6 residues within 4Å: Chain A: L.78, G.79, A.80, N.81, K.85 Ligands: CIT.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.80, A:N.81, A:N.81 Water bridges: A:K.85, A:K.85 Salt bridges: A:K.85 SO4.8: 5 residues within 4Å: Chain A: R.28, R.29 Chain B: R.28, R.29 Ligands: SO4.16 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Water bridges: A:R.28, A:R.28, A:R.28, A:R.28, B:R.28, B:R.28, B:R.28 Salt bridges: A:R.28, A:R.29, B:R.28, B:R.29 SO4.12: 3 residues within 4Å: Chain B: K.57, R.61 Chain D: Q.35 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain D Water bridges: B:K.57, B:K.57, B:H.60, B:H.60, B:R.61, B:R.61 Salt bridges: B:K.57, B:R.61 Hydrogen bonds: D:Q.35 SO4.13: 7 residues within 4Å: Chain B: L.27, R.28, A.31, R.40, Y.43 Chain C: Q.24, R.28 10 PLIP interactions: 1 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:R.28, B:Y.43 Water bridges: B:R.28, B:R.28, B:R.40, B:R.40, B:R.40, B:R.40, B:Y.43 Salt bridges: B:R.40 SO4.14: 6 residues within 4Å: Chain B: L.78, G.79, A.80, N.81, K.85 Ligands: CIT.15 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.80, B:N.81, B:N.81 Water bridges: B:K.85, B:K.85 Salt bridges: B:K.85 SO4.16: 5 residues within 4Å: Chain A: R.28, R.29 Chain B: R.28, R.29 Ligands: SO4.8 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Water bridges: A:R.28, A:R.28, A:R.28, B:R.28, B:R.28, B:R.28, B:R.28 Salt bridges: A:R.28, A:R.29, B:R.28, B:R.29 SO4.19: 6 residues within 4Å: Chain C: L.78, G.79, A.80, N.81, K.85 Ligands: CIT.18 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.80, C:N.81, C:N.81 Salt bridges: C:K.85 SO4.22: 6 residues within 4Å: Chain D: L.78, G.79, A.80, N.81, K.85 Ligands: CIT.21 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.80, D:N.81, D:N.81 Salt bridges: D:K.85

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

CIT.7: 5 residues within 4Å: Chain A: G.79, A.80, N.81, K.85 Ligands: SO4.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.80 Hydrogen bonds: A:A.80, A:N.81, A:N.81, A:K.85 Salt bridges: A:K.85, A:K.85 CIT.15: 5 residues within 4Å: Chain B: G.79, A.80, N.81, K.85 Ligands: SO4.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.80 Hydrogen bonds: B:A.80, B:N.81, B:N.81, B:K.85 Salt bridges: B:K.85, B:K.85 CIT.17: 5 residues within 4Å: Chain C: P.21, G.22, R.25, R.26, R.29 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.22 Water bridges: C:R.25, C:R.29 Salt bridges: C:R.26, C:R.29, C:R.29 CIT.18: 6 residues within 4Å: Chain C: L.78, G.79, A.80, N.81, K.85 Ligands: SO4.19 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:L.78, C:A.80, C:N.81, C:N.81, C:K.85 Salt bridges: C:K.85 CIT.20: 5 residues within 4Å: Chain D: P.21, G.22, R.25, R.26, R.29 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.22 Water bridges: D:R.25, D:R.29 Salt bridges: D:R.26, D:R.29, D:R.29 CIT.21: 6 residues within 4Å: Chain D: L.78, G.79, A.80, N.81, K.85 Ligands: SO4.22 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:L.78, D:A.80, D:N.81, D:N.81, D:K.85 Salt bridges: D:K.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Samai, P. et al., Structure of a CRISPR-associated protein Cas2 from Desulfovibrio vulgaris. Acta Crystallogr.,Sect.F (2010)

Release Date

2010-12-22

Peptides

CRISPR-associated protein Cas2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

CRISPR-associated protein Cas2

Related Entries With Identical Sequence