SMTL ID : 5zs3.1

Small heat shock protein from M. marinum:Form-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-12-mer

Ligands

12 x GLY- ARG- LEU- LEU- PRO: GLY-ARG-LEU-LEU-PRO(Non-covalent)

GLY-ARG-LEU-LEU-PRO.1: 13 residues within 4Å: Chain A: R.34, F.39, L.91, V.92, L.93, G.94, L.97, V.117 Chain C: L.78 Chain K: V.61, Q.90, V.92 Ligands: NA.8 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain K Hydrophobic interactions: A:F.39, A:L.91, A:V.92, K:V.92 Hydrogen bonds: A:R.34, A:R.34, A:V.92, A:G.94, K:Q.90, K:Q.90 GLY-ARG-LEU-LEU-PRO.9: 13 residues within 4Å: Chain B: R.34, F.39, L.91, V.92, L.93, G.94, L.97, V.117 Chain D: L.78 Chain J: V.61, Q.90, V.92 Ligands: NA.16 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain J Hydrophobic interactions: B:F.39, B:L.91, B:V.92, J:V.92 Hydrogen bonds: B:R.34, B:R.34, B:V.92, B:G.94, J:Q.90, J:Q.90 GLY-ARG-LEU-LEU-PRO.17: 13 residues within 4Å: Chain A: L.78 Chain C: R.34, F.39, L.91, V.92, L.93, G.94, L.97, V.117 Chain L: V.61, Q.90, V.92 Ligands: NA.24 10 PLIP interactions: 3 interactions with chain L, 7 interactions with chain C Hydrophobic interactions: L:V.92, C:F.39, C:L.91, C:V.92 Hydrogen bonds: L:Q.90, L:Q.90, C:R.34, C:R.34, C:V.92, C:G.94 GLY-ARG-LEU-LEU-PRO.25: 13 residues within 4Å: Chain B: L.78 Chain D: R.34, F.39, L.91, V.92, L.93, G.94, L.97, V.117 Chain I: V.61, Q.90, V.92 Ligands: NA.32 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain I Hydrophobic interactions: D:F.39, D:L.91, D:V.92, I:V.92 Hydrogen bonds: D:R.34, D:R.34, D:V.92, D:G.94, I:Q.90, I:Q.90 GLY-ARG-LEU-LEU-PRO.33: 13 residues within 4Å: Chain C: V.61, Q.90, V.92 Chain E: R.34, F.39, L.91, V.92, L.93, G.94, L.97, V.117 Chain G: L.78 Ligands: NA.40 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain E Hydrophobic interactions: C:V.92, E:F.39, E:L.91, E:V.92 Hydrogen bonds: C:Q.90, C:Q.90, E:R.34, E:R.34, E:V.92, E:G.94 GLY-ARG-LEU-LEU-PRO.41: 13 residues within 4Å: Chain B: V.61, Q.90, V.92 Chain F: R.34, F.39, L.91, V.92, L.93, G.94, L.97, V.117 Chain H: L.78 Ligands: NA.48 10 PLIP interactions: 7 interactions with chain F, 3 interactions with chain B Hydrophobic interactions: F:F.39, F:L.91, F:V.92, B:V.92 Hydrogen bonds: F:R.34, F:R.34, F:V.92, F:G.94, B:Q.90, B:Q.90 GLY-ARG-LEU-LEU-PRO.49: 13 residues within 4Å: Chain D: V.61, Q.90, V.92 Chain E: L.78 Chain G: R.34, F.39, L.91, V.92, L.93, G.94, L.97, V.117 Ligands: NA.56 10 PLIP interactions: 7 interactions with chain G, 3 interactions with chain D Hydrophobic interactions: G:F.39, G:L.91, G:V.92, D:V.92 Hydrogen bonds: G:R.34, G:R.34, G:V.92, G:G.94, D:Q.90, D:Q.90 GLY-ARG-LEU-LEU-PRO.57: 13 residues within 4Å: Chain A: V.61, Q.90, V.92 Chain F: L.78 Chain H: R.34, F.39, L.91, V.92, L.93, G.94, L.97, V.117 Ligands: NA.64 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain H Hydrophobic interactions: A:V.92, H:F.39, H:L.91, H:V.92 Hydrogen bonds: A:Q.90, A:Q.90, H:R.34, H:R.34, H:V.92, H:G.94 GLY-ARG-LEU-LEU-PRO.65: 13 residues within 4Å: Chain G: V.61, Q.90, V.92 Chain I: R.34, F.39, L.91, V.92, L.93, G.94, L.97, V.117 Chain K: L.78 Ligands: NA.72 10 PLIP interactions: 7 interactions with chain I, 3 interactions with chain G Hydrophobic interactions: I:F.39, I:L.91, I:V.92, G:V.92 Hydrogen bonds: I:R.34, I:R.34, I:V.92, I:G.94, G:Q.90, G:Q.90 GLY-ARG-LEU-LEU-PRO.73: 13 residues within 4Å: Chain F: V.61, Q.90, V.92 Chain J: R.34, F.39, L.91, V.92, L.93, G.94, L.97, V.117 Chain L: L.78 Ligands: NA.80 10 PLIP interactions: 7 interactions with chain J, 3 interactions with chain F Hydrophobic interactions: J:F.39, J:L.91, J:V.92, F:V.92 Hydrogen bonds: J:R.34, J:R.34, J:V.92, J:G.94, F:Q.90, F:Q.90 GLY-ARG-LEU-LEU-PRO.81: 13 residues within 4Å: Chain H: V.61, Q.90, V.92 Chain I: L.78 Chain K: R.34, F.39, L.91, V.92, L.93, G.94, L.97, V.117 Ligands: NA.88 10 PLIP interactions: 3 interactions with chain H, 7 interactions with chain K Hydrophobic interactions: H:V.92, K:F.39, K:L.91, K:V.92 Hydrogen bonds: H:Q.90, H:Q.90, K:R.34, K:R.34, K:V.92, K:G.94 GLY-ARG-LEU-LEU-PRO.89: 13 residues within 4Å: Chain E: V.61, Q.90, V.92 Chain J: L.78 Chain L: R.34, F.39, L.91, V.92, L.93, G.94, L.97, V.117 Ligands: NA.96 10 PLIP interactions: 7 interactions with chain L, 3 interactions with chain E Hydrophobic interactions: L:F.39, L:L.91, L:V.92, E:V.92 Hydrogen bonds: L:R.34, L:R.34, L:V.92, L:G.94, E:Q.90, E:Q.90

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

NA.2: 4 residues within 4Å: Chain A: E.76, L.78 Chain C: W.33, R.34 Ligand excluded by PLIP NA.8: 5 residues within 4Å: Chain A: Q.90, L.91, V.92 Ligands: GLY-ARG-LEU-LEU-PRO.1, GLY-ARG-LEU-LEU-PRO.1 Ligand excluded by PLIP NA.10: 4 residues within 4Å: Chain B: E.76, L.78 Chain D: W.33, R.34 Ligand excluded by PLIP NA.16: 5 residues within 4Å: Chain B: Q.90, L.91, V.92 Ligands: GLY-ARG-LEU-LEU-PRO.9, GLY-ARG-LEU-LEU-PRO.9 Ligand excluded by PLIP NA.18: 4 residues within 4Å: Chain A: W.33, R.34 Chain C: E.76, L.78 Ligand excluded by PLIP NA.24: 5 residues within 4Å: Chain C: Q.90, L.91, V.92 Ligands: GLY-ARG-LEU-LEU-PRO.17, GLY-ARG-LEU-LEU-PRO.17 Ligand excluded by PLIP NA.26: 4 residues within 4Å: Chain B: W.33, R.34 Chain D: E.76, L.78 Ligand excluded by PLIP NA.32: 5 residues within 4Å: Chain D: Q.90, L.91, V.92 Ligands: GLY-ARG-LEU-LEU-PRO.25, GLY-ARG-LEU-LEU-PRO.25 Ligand excluded by PLIP NA.34: 4 residues within 4Å: Chain E: E.76, L.78 Chain G: W.33, R.34 Ligand excluded by PLIP NA.40: 5 residues within 4Å: Chain E: Q.90, L.91, V.92 Ligands: GLY-ARG-LEU-LEU-PRO.33, GLY-ARG-LEU-LEU-PRO.33 Ligand excluded by PLIP NA.42: 4 residues within 4Å: Chain F: E.76, L.78 Chain H: W.33, R.34 Ligand excluded by PLIP NA.48: 5 residues within 4Å: Chain F: Q.90, L.91, V.92 Ligands: GLY-ARG-LEU-LEU-PRO.41, GLY-ARG-LEU-LEU-PRO.41 Ligand excluded by PLIP NA.50: 4 residues within 4Å: Chain E: W.33, R.34 Chain G: E.76, L.78 Ligand excluded by PLIP NA.56: 5 residues within 4Å: Chain G: Q.90, L.91, V.92 Ligands: GLY-ARG-LEU-LEU-PRO.49, GLY-ARG-LEU-LEU-PRO.49 Ligand excluded by PLIP NA.58: 4 residues within 4Å: Chain F: W.33, R.34 Chain H: E.76, L.78 Ligand excluded by PLIP NA.64: 5 residues within 4Å: Chain H: Q.90, L.91, V.92 Ligands: GLY-ARG-LEU-LEU-PRO.57, GLY-ARG-LEU-LEU-PRO.57 Ligand excluded by PLIP NA.66: 4 residues within 4Å: Chain I: E.76, L.78 Chain K: W.33, R.34 Ligand excluded by PLIP NA.72: 5 residues within 4Å: Chain I: Q.90, L.91, V.92 Ligands: GLY-ARG-LEU-LEU-PRO.65, GLY-ARG-LEU-LEU-PRO.65 Ligand excluded by PLIP NA.74: 4 residues within 4Å: Chain J: E.76, L.78 Chain L: W.33, R.34 Ligand excluded by PLIP NA.80: 5 residues within 4Å: Chain J: Q.90, L.91, V.92 Ligands: GLY-ARG-LEU-LEU-PRO.73, GLY-ARG-LEU-LEU-PRO.73 Ligand excluded by PLIP NA.82: 4 residues within 4Å: Chain I: W.33, R.34 Chain K: E.76, L.78 Ligand excluded by PLIP NA.88: 5 residues within 4Å: Chain K: Q.90, L.91, V.92 Ligands: GLY-ARG-LEU-LEU-PRO.81, GLY-ARG-LEU-LEU-PRO.81 Ligand excluded by PLIP NA.90: 4 residues within 4Å: Chain J: W.33, R.34 Chain L: E.76, L.78 Ligand excluded by PLIP NA.96: 5 residues within 4Å: Chain L: Q.90, L.91, V.92 Ligands: GLY-ARG-LEU-LEU-PRO.89, GLY-ARG-LEU-LEU-PRO.89 Ligand excluded by PLIP

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

SO4.3: 5 residues within 4Å: Chain A: N.60 Chain H: N.60 Chain K: N.60 Ligands: SO4.59, SO4.83 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain H, 1 interactions with chain K Hydrogen bonds: A:N.60, H:N.60, K:N.60 SO4.11: 5 residues within 4Å: Chain B: N.60 Chain F: N.60 Chain J: N.60 Ligands: SO4.43, SO4.75 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain B, 1 interactions with chain F Hydrogen bonds: J:N.60, B:N.60, F:N.60 SO4.19: 5 residues within 4Å: Chain C: N.60 Chain E: N.60 Chain L: N.60 Ligands: SO4.35, SO4.91 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain L, 1 interactions with chain E Hydrogen bonds: C:N.60, L:N.60, E:N.60 SO4.27: 5 residues within 4Å: Chain D: N.60 Chain G: N.60 Chain I: N.60 Ligands: SO4.51, SO4.67 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain I, 1 interactions with chain G Hydrogen bonds: D:N.60, I:N.60, G:N.60 SO4.35: 5 residues within 4Å: Chain C: N.60 Chain E: N.60 Chain L: N.60 Ligands: SO4.19, SO4.91 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain L, 1 interactions with chain E Hydrogen bonds: C:N.60, L:N.60, E:N.60 SO4.43: 5 residues within 4Å: Chain B: N.60 Chain F: N.60 Chain J: N.60 Ligands: SO4.11, SO4.75 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain B, 1 interactions with chain F Hydrogen bonds: J:N.60, B:N.60, F:N.60 SO4.51: 5 residues within 4Å: Chain D: N.60 Chain G: N.60 Chain I: N.60 Ligands: SO4.27, SO4.67 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain I, 1 interactions with chain G Hydrogen bonds: D:N.60, I:N.60, G:N.60 SO4.59: 5 residues within 4Å: Chain A: N.60 Chain H: N.60 Chain K: N.60 Ligands: SO4.3, SO4.83 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain H, 1 interactions with chain K Hydrogen bonds: A:N.60, H:N.60, K:N.60 SO4.67: 5 residues within 4Å: Chain D: N.60 Chain G: N.60 Chain I: N.60 Ligands: SO4.27, SO4.51 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain I, 1 interactions with chain G Hydrogen bonds: D:N.60, I:N.60, G:N.60 SO4.75: 5 residues within 4Å: Chain B: N.60 Chain F: N.60 Chain J: N.60 Ligands: SO4.11, SO4.43 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain B, 1 interactions with chain F Hydrogen bonds: J:N.60, B:N.60, F:N.60 SO4.83: 5 residues within 4Å: Chain A: N.60 Chain H: N.60 Chain K: N.60 Ligands: SO4.3, SO4.59 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain H, 1 interactions with chain K Hydrogen bonds: A:N.60, H:N.60, K:N.60 SO4.91: 5 residues within 4Å: Chain C: N.60 Chain E: N.60 Chain L: N.60 Ligands: SO4.19, SO4.35 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain L, 1 interactions with chain E Hydrogen bonds: C:N.60, L:N.60, E:N.60

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

CL.4: 2 residues within 4Å: Chain A: A.26, V.27 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: R.84 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: E.108 Chain C: E.108 Ligands: CL.22 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: R.75 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: A.26, V.27 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: R.84 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: E.108 Chain D: E.108 Ligands: CL.30 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: R.75 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain C: A.26, V.27 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain C: R.84 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain A: E.108 Chain C: E.108 Ligands: CL.6 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain C: R.75 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain D: A.26, V.27 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain D: R.84 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain B: E.108 Chain D: E.108 Ligands: CL.14 Ligand excluded by PLIP CL.31: 1 residues within 4Å: Chain D: R.75 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain E: A.26, V.27 Ligand excluded by PLIP CL.37: 1 residues within 4Å: Chain E: R.84 Ligand excluded by PLIP CL.38: 3 residues within 4Å: Chain E: E.108 Chain G: E.108 Ligands: CL.54 Ligand excluded by PLIP CL.39: 1 residues within 4Å: Chain E: R.75 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain F: A.26, V.27 Ligand excluded by PLIP CL.45: 1 residues within 4Å: Chain F: R.84 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain F: E.108 Chain H: E.108 Ligands: CL.62 Ligand excluded by PLIP CL.47: 1 residues within 4Å: Chain F: R.75 Ligand excluded by PLIP CL.52: 2 residues within 4Å: Chain G: A.26, V.27 Ligand excluded by PLIP CL.53: 1 residues within 4Å: Chain G: R.84 Ligand excluded by PLIP CL.54: 3 residues within 4Å: Chain E: E.108 Chain G: E.108 Ligands: CL.38 Ligand excluded by PLIP CL.55: 1 residues within 4Å: Chain G: R.75 Ligand excluded by PLIP CL.60: 2 residues within 4Å: Chain H: A.26, V.27 Ligand excluded by PLIP CL.61: 1 residues within 4Å: Chain H: R.84 Ligand excluded by PLIP CL.62: 3 residues within 4Å: Chain F: E.108 Chain H: E.108 Ligands: CL.46 Ligand excluded by PLIP CL.63: 1 residues within 4Å: Chain H: R.75 Ligand excluded by PLIP CL.68: 2 residues within 4Å: Chain I: A.26, V.27 Ligand excluded by PLIP CL.69: 1 residues within 4Å: Chain I: R.84 Ligand excluded by PLIP CL.70: 3 residues within 4Å: Chain I: E.108 Chain K: E.108 Ligands: CL.86 Ligand excluded by PLIP CL.71: 1 residues within 4Å: Chain I: R.75 Ligand excluded by PLIP CL.76: 2 residues within 4Å: Chain J: A.26, V.27 Ligand excluded by PLIP CL.77: 1 residues within 4Å: Chain J: R.84 Ligand excluded by PLIP CL.78: 3 residues within 4Å: Chain J: E.108 Chain L: E.108 Ligands: CL.94 Ligand excluded by PLIP CL.79: 1 residues within 4Å: Chain J: R.75 Ligand excluded by PLIP CL.84: 2 residues within 4Å: Chain K: A.26, V.27 Ligand excluded by PLIP CL.85: 1 residues within 4Å: Chain K: R.84 Ligand excluded by PLIP CL.86: 3 residues within 4Å: Chain I: E.108 Chain K: E.108 Ligands: CL.70 Ligand excluded by PLIP CL.87: 1 residues within 4Å: Chain K: R.75 Ligand excluded by PLIP CL.92: 2 residues within 4Å: Chain L: A.26, V.27 Ligand excluded by PLIP CL.93: 1 residues within 4Å: Chain L: R.84 Ligand excluded by PLIP CL.94: 3 residues within 4Å: Chain J: E.108 Chain L: E.108 Ligands: CL.78 Ligand excluded by PLIP CL.95: 1 residues within 4Å: Chain L: R.75 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhandari, S. et al., Dodecameric structure of a small heat shock protein from Mycobacterium marinum M. Proteins (2019)

Release Date

2019-01-30

Peptides

Molecular chaperone (Small heat shock protein): ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

Molecular chaperone (Small heat shock protein)

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