SMTL ID : 3cgm.2 (1 other biounit)

Crystal structure of thermophilic SlyD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-hexamer

Ligands

36 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.1: 6 residues within 4Å: Chain A: L.36, I.37, Y.63, F.128 Ligands: GOL.8, GOL.9 Ligand excluded by PLIP SCN.2: 5 residues within 4Å: Chain A: Y.29, L.30, N.35, H.147, A.148 Ligand excluded by PLIP SCN.3: 3 residues within 4Å: Chain A: P.65, D.67, P.68 Ligand excluded by PLIP SCN.4: 2 residues within 4Å: Chain A: K.134 Chain E: V.133 Ligand excluded by PLIP SCN.5: 2 residues within 4Å: Chain A: A.78, F.79 Ligand excluded by PLIP SCN.7: 2 residues within 4Å: Chain A: R.47, F.53 Ligand excluded by PLIP SCN.10: 6 residues within 4Å: Chain B: L.36, I.37, Y.63, F.128 Ligands: GOL.17, GOL.18 Ligand excluded by PLIP SCN.11: 5 residues within 4Å: Chain B: Y.29, L.30, N.35, H.147, A.148 Ligand excluded by PLIP SCN.12: 3 residues within 4Å: Chain B: P.65, D.67, P.68 Ligand excluded by PLIP SCN.13: 2 residues within 4Å: Chain B: K.134 Chain D: V.133 Ligand excluded by PLIP SCN.14: 2 residues within 4Å: Chain B: A.78, F.79 Ligand excluded by PLIP SCN.16: 2 residues within 4Å: Chain B: R.47, F.53 Ligand excluded by PLIP SCN.19: 6 residues within 4Å: Chain C: L.36, I.37, Y.63, F.128 Ligands: GOL.26, GOL.27 Ligand excluded by PLIP SCN.20: 5 residues within 4Å: Chain C: Y.29, L.30, N.35, H.147, A.148 Ligand excluded by PLIP SCN.21: 3 residues within 4Å: Chain C: P.65, D.67, P.68 Ligand excluded by PLIP SCN.22: 2 residues within 4Å: Chain A: V.133 Chain C: K.134 Ligand excluded by PLIP SCN.23: 2 residues within 4Å: Chain C: A.78, F.79 Ligand excluded by PLIP SCN.25: 2 residues within 4Å: Chain C: R.47, F.53 Ligand excluded by PLIP SCN.28: 6 residues within 4Å: Chain D: L.36, I.37, Y.63, F.128 Ligands: GOL.35, GOL.36 Ligand excluded by PLIP SCN.29: 5 residues within 4Å: Chain D: Y.29, L.30, N.35, H.147, A.148 Ligand excluded by PLIP SCN.30: 3 residues within 4Å: Chain D: P.65, D.67, P.68 Ligand excluded by PLIP SCN.31: 2 residues within 4Å: Chain D: K.134 Chain F: V.133 Ligand excluded by PLIP SCN.32: 2 residues within 4Å: Chain D: A.78, F.79 Ligand excluded by PLIP SCN.34: 2 residues within 4Å: Chain D: R.47, F.53 Ligand excluded by PLIP SCN.37: 6 residues within 4Å: Chain E: L.36, I.37, Y.63, F.128 Ligands: GOL.44, GOL.45 Ligand excluded by PLIP SCN.38: 5 residues within 4Å: Chain E: Y.29, L.30, N.35, H.147, A.148 Ligand excluded by PLIP SCN.39: 3 residues within 4Å: Chain E: P.65, D.67, P.68 Ligand excluded by PLIP SCN.40: 2 residues within 4Å: Chain C: V.133 Chain E: K.134 Ligand excluded by PLIP SCN.41: 2 residues within 4Å: Chain E: A.78, F.79 Ligand excluded by PLIP SCN.43: 2 residues within 4Å: Chain E: R.47, F.53 Ligand excluded by PLIP SCN.46: 6 residues within 4Å: Chain F: L.36, I.37, Y.63, F.128 Ligands: GOL.53, GOL.54 Ligand excluded by PLIP SCN.47: 5 residues within 4Å: Chain F: Y.29, L.30, N.35, H.147, A.148 Ligand excluded by PLIP SCN.48: 3 residues within 4Å: Chain F: P.65, D.67, P.68 Ligand excluded by PLIP SCN.49: 2 residues within 4Å: Chain B: V.133 Chain F: K.134 Ligand excluded by PLIP SCN.50: 2 residues within 4Å: Chain F: A.78, F.79 Ligand excluded by PLIP SCN.52: 2 residues within 4Å: Chain F: R.47, F.53 Ligand excluded by PLIP

6 x NI: NICKEL (II) ION(Non-covalent)

NI.6: 6 residues within 4Å: Chain A: H.145, H.147, H.149, H.155, H.157 Chain B: H.153 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.145, A:H.147, A:H.149, A:H.155, A:H.157, B:H.153 NI.15: 6 residues within 4Å: Chain A: H.153 Chain B: H.145, H.147, H.149, H.155, H.157 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.145, B:H.147, B:H.149, B:H.155, B:H.157, A:H.153 NI.24: 6 residues within 4Å: Chain C: H.145, H.147, H.149, H.155, H.157 Chain D: H.153 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Metal complexes: C:H.145, C:H.147, C:H.149, C:H.155, C:H.157, D:H.153 NI.33: 6 residues within 4Å: Chain C: H.153 Chain D: H.145, H.147, H.149, H.155, H.157 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Metal complexes: D:H.145, D:H.147, D:H.149, D:H.155, D:H.157, C:H.153 NI.42: 6 residues within 4Å: Chain E: H.145, H.147, H.149, H.155, H.157 Chain F: H.153 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain F Metal complexes: E:H.145, E:H.147, E:H.149, E:H.155, E:H.157, F:H.153 NI.51: 6 residues within 4Å: Chain E: H.153 Chain F: H.145, H.147, H.149, H.155, H.157 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain E Metal complexes: F:H.145, F:H.147, F:H.149, F:H.155, F:H.157, E:H.153

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: D.23, L.27, L.36 Ligands: SCN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.23, A:D.23 GOL.9: 6 residues within 4Å: Chain A: R.34, N.35, L.36, I.37, Y.63 Ligands: SCN.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.34, A:Y.63, A:Y.63 GOL.17: 4 residues within 4Å: Chain B: D.23, L.27, L.36 Ligands: SCN.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.23 Water bridges: B:Y.63 GOL.18: 6 residues within 4Å: Chain B: R.34, N.35, L.36, I.37, Y.63 Ligands: SCN.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.34, B:Y.63 GOL.26: 4 residues within 4Å: Chain C: D.23, L.27, L.36 Ligands: SCN.19 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.23, C:D.23 GOL.27: 6 residues within 4Å: Chain C: R.34, N.35, L.36, I.37, Y.63 Ligands: SCN.19 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.34, C:Y.63, C:Y.63 GOL.35: 4 residues within 4Å: Chain D: D.23, L.27, L.36 Ligands: SCN.28 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.23 Water bridges: D:Y.63 GOL.36: 6 residues within 4Å: Chain D: R.34, N.35, L.36, I.37, Y.63 Ligands: SCN.28 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.34, D:Y.63 GOL.44: 4 residues within 4Å: Chain E: D.23, L.27, L.36 Ligands: SCN.37 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.23, E:D.23 GOL.45: 6 residues within 4Å: Chain E: R.34, N.35, L.36, I.37, Y.63 Ligands: SCN.37 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.34, E:Y.63, E:Y.63 GOL.53: 4 residues within 4Å: Chain F: D.23, L.27, L.36 Ligands: SCN.46 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.23 Water bridges: F:Y.63 GOL.54: 6 residues within 4Å: Chain F: R.34, N.35, L.36, I.37, Y.63 Ligands: SCN.46 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.34, F:Y.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loew, C. et al., Crystal Structure Determination and Functional Characterization of the Metallochaperone SlyD from Thermus thermophilus. J.Mol.Biol. (2010)

Release Date

2009-03-10

Peptides

Peptidyl-prolyl cis-trans isomerase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Peptidyl-prolyl cis-trans isomerase

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