SMTL ID : 2zqm.2 (1 other biounit)

Crystal structure of the prefoldin beta subunit from Thermococcus strain KS-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-octamer

Ligands

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

CIT.1: 9 residues within 4Å: Chain A: A.88, R.91, Q.92, K.95 Chain G: Y.18, K.99 Ligands: GOL.2, GOL.4, GOL.40 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain G Hydrogen bonds: A:Q.92, G:Y.18, G:Y.18 Water bridges: A:K.95 Salt bridges: A:R.91, A:K.95, A:K.95, G:K.99, G:K.99 CIT.7: 9 residues within 4Å: Chain B: A.88, R.91, Q.92, K.95 Chain H: Y.18, K.99 Ligands: GOL.8, GOL.10, GOL.46 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain H Hydrogen bonds: B:Q.92, H:Y.18, H:Y.18 Water bridges: B:K.95 Salt bridges: B:R.91, B:K.95, B:K.95, H:K.99, H:K.99 CIT.13: 9 residues within 4Å: Chain C: A.88, R.91, Q.92, K.95 Chain E: Y.18, K.99 Ligands: GOL.14, GOL.16, GOL.28 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain E Hydrogen bonds: C:Q.92, E:Y.18, E:Y.18 Water bridges: C:K.95 Salt bridges: C:R.91, C:K.95, C:K.95, E:K.99, E:K.99 CIT.19: 9 residues within 4Å: Chain D: A.88, R.91, Q.92, K.95 Chain F: Y.18, K.99 Ligands: GOL.20, GOL.22, GOL.34 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain F Hydrogen bonds: D:Q.92, F:Y.18, F:Y.18 Water bridges: D:K.95 Salt bridges: D:R.91, D:K.95, D:K.95, F:K.99, F:K.99 CIT.25: 9 residues within 4Å: Chain C: Y.18, K.99 Chain E: A.88, R.91, Q.92, K.95 Ligands: GOL.16, GOL.26, GOL.28 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain E Hydrogen bonds: C:Y.18, E:Q.92 Salt bridges: C:K.99, C:K.99, E:R.91, E:K.95, E:K.95 Water bridges: E:K.95 CIT.31: 9 residues within 4Å: Chain D: Y.18, K.99 Chain F: A.88, R.91, Q.92, K.95 Ligands: GOL.22, GOL.32, GOL.34 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:Q.92, D:Y.18 Water bridges: F:K.95 Salt bridges: F:R.91, F:K.95, F:K.95, D:K.99, D:K.99 CIT.37: 9 residues within 4Å: Chain A: Y.18, K.99 Chain G: A.88, R.91, Q.92, K.95 Ligands: GOL.4, GOL.38, GOL.40 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain G Hydrogen bonds: A:Y.18, G:Q.92 Salt bridges: A:K.99, A:K.99, G:R.91, G:K.95, G:K.95 Water bridges: G:K.95 CIT.43: 9 residues within 4Å: Chain B: Y.18, K.99 Chain H: A.88, R.91, Q.92, K.95 Ligands: GOL.10, GOL.44, GOL.46 8 PLIP interactions: 5 interactions with chain H, 3 interactions with chain B Hydrogen bonds: H:Q.92, B:Y.18 Water bridges: H:K.95 Salt bridges: H:R.91, H:K.95, H:K.95, B:K.99, B:K.99

40 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: V.84, R.91 Chain G: Q.14, L.103 Ligands: CIT.1 Ligand excluded by PLIP GOL.3: 8 residues within 4Å: Chain A: Q.21, V.25, Q.92, L.96 Chain G: Q.21, Q.92, L.96 Ligands: GOL.39 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: K.95, K.99 Chain G: K.95, K.99 Ligands: CIT.1, CIT.37, GOL.40 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: D.52, A.53, V.54, V.55, K.65, T.66, T.67 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: Y.56 Chain B: Y.56 Chain C: Y.56 Chain D: Y.56 Ligands: GOL.12, GOL.18, GOL.24 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain B: V.84, R.91 Chain H: Q.14, L.103 Ligands: CIT.7 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain B: Q.21, V.25, Q.92, L.96 Chain H: Q.21, Q.92, L.96 Ligands: GOL.45 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain B: K.95, K.99 Chain H: K.95, K.99 Ligands: CIT.7, CIT.43, GOL.46 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain B: D.52, A.53, V.54, V.55, K.65, T.66, T.67 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain A: Y.56 Chain B: Y.56 Chain C: Y.56 Chain D: Y.56 Ligands: GOL.6, GOL.18, GOL.24 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain C: V.84, R.91 Chain E: Q.14, L.103 Ligands: CIT.13 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain C: Q.21, V.25, Q.92, L.96 Chain E: Q.21, Q.92, L.96 Ligands: GOL.27 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain C: K.95, K.99 Chain E: K.95, K.99 Ligands: CIT.13, CIT.25, GOL.28 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain C: D.52, A.53, V.54, V.55, K.65, T.66, T.67 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain A: Y.56 Chain B: Y.56 Chain C: Y.56 Chain D: Y.56 Ligands: GOL.6, GOL.12, GOL.24 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain D: V.84, R.91 Chain F: Q.14, L.103 Ligands: CIT.19 Ligand excluded by PLIP GOL.21: 8 residues within 4Å: Chain D: Q.21, V.25, Q.92, L.96 Chain F: Q.21, Q.92, L.96 Ligands: GOL.33 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain D: K.95, K.99 Chain F: K.95, K.99 Ligands: CIT.19, CIT.31, GOL.34 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain D: D.52, A.53, V.54, V.55, K.65, T.66, T.67 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain A: Y.56 Chain B: Y.56 Chain C: Y.56 Chain D: Y.56 Ligands: GOL.6, GOL.12, GOL.18 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain C: Q.14, L.103 Chain E: V.84, R.91 Ligands: CIT.25 Ligand excluded by PLIP GOL.27: 8 residues within 4Å: Chain C: Q.21, Q.92, L.96 Chain E: Q.21, V.25, Q.92, L.96 Ligands: GOL.15 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain C: K.95, K.99 Chain E: K.95, K.99 Ligands: CIT.13, GOL.16, CIT.25 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain E: D.52, A.53, V.54, V.55, K.65, T.66, T.67 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain E: Y.56 Chain F: Y.56 Chain G: Y.56 Chain H: Y.56 Ligands: GOL.36, GOL.42, GOL.48 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain D: Q.14, L.103 Chain F: V.84, R.91 Ligands: CIT.31 Ligand excluded by PLIP GOL.33: 8 residues within 4Å: Chain D: Q.21, Q.92, L.96 Chain F: Q.21, V.25, Q.92, L.96 Ligands: GOL.21 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain D: K.95, K.99 Chain F: K.95, K.99 Ligands: CIT.19, GOL.22, CIT.31 Ligand excluded by PLIP GOL.35: 7 residues within 4Å: Chain F: D.52, A.53, V.54, V.55, K.65, T.66, T.67 Ligand excluded by PLIP GOL.36: 7 residues within 4Å: Chain E: Y.56 Chain F: Y.56 Chain G: Y.56 Chain H: Y.56 Ligands: GOL.30, GOL.42, GOL.48 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain A: Q.14, L.103 Chain G: V.84, R.91 Ligands: CIT.37 Ligand excluded by PLIP GOL.39: 8 residues within 4Å: Chain A: Q.21, Q.92, L.96 Chain G: Q.21, V.25, Q.92, L.96 Ligands: GOL.3 Ligand excluded by PLIP GOL.40: 7 residues within 4Å: Chain A: K.95, K.99 Chain G: K.95, K.99 Ligands: CIT.1, GOL.4, CIT.37 Ligand excluded by PLIP GOL.41: 7 residues within 4Å: Chain G: D.52, A.53, V.54, V.55, K.65, T.66, T.67 Ligand excluded by PLIP GOL.42: 7 residues within 4Å: Chain E: Y.56 Chain F: Y.56 Chain G: Y.56 Chain H: Y.56 Ligands: GOL.30, GOL.36, GOL.48 Ligand excluded by PLIP GOL.44: 5 residues within 4Å: Chain B: Q.14, L.103 Chain H: V.84, R.91 Ligands: CIT.43 Ligand excluded by PLIP GOL.45: 8 residues within 4Å: Chain B: Q.21, Q.92, L.96 Chain H: Q.21, V.25, Q.92, L.96 Ligands: GOL.9 Ligand excluded by PLIP GOL.46: 7 residues within 4Å: Chain B: K.95, K.99 Chain H: K.95, K.99 Ligands: CIT.7, GOL.10, CIT.43 Ligand excluded by PLIP GOL.47: 7 residues within 4Å: Chain H: D.52, A.53, V.54, V.55, K.65, T.66, T.67 Ligand excluded by PLIP GOL.48: 7 residues within 4Å: Chain E: Y.56 Chain F: Y.56 Chain G: Y.56 Chain H: Y.56 Ligands: GOL.30, GOL.36, GOL.42 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kida, H. et al., Structural and molecular characterization of the prefoldin beta subunit from Thermococcus strain KS-1. J.Mol.Biol. (2008)

Release Date

2008-08-26

Peptides

Prefoldin beta subunit 1: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

Prefoldin beta subunit 1

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