SMTL ID : 8wt1.2 (1 other biounit)

Crystal structure of S9 carboxypeptidase from Geobacillus sterothermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: R.46, D.47, V.60, M.94, K.95, A.334, K.335 Ligand excluded by PLIP SO4.2: 2 residues within 4Å: Chain A: R.355, R.357 Ligand excluded by PLIP SO4.3: 7 residues within 4Å: Chain A: G.470, G.549, S.550, R.573, H.663, R.667 Ligands: GOL.12 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: Y.438, R.439, K.535 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: G.515, R.606 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: F.194, L.195, D.196, G.197, K.198 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: S.63, H.73, Q.85 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: R.416, R.419 Ligand excluded by PLIP SO4.15: 7 residues within 4Å: Chain B: R.46, D.47, V.60, M.94, K.95, A.334, K.335 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain B: G.470, G.549, S.550, R.573, H.663, R.667 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain B: R.355, R.357 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain B: L.195, D.196, G.197, K.198 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain B: R.312, L.365 Ligand excluded by PLIP SO4.20: 9 residues within 4Å: Chain B: S.44, R.46, K.62, D.329, T.330, H.331, A.332, D.333, R.667 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain B: R.416, R.419 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain B: T.437, Y.438, R.439, K.535 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain B: Y.186, D.245, R.250, Y.589, F.590 Ligand excluded by PLIP SO4.30: 7 residues within 4Å: Chain C: R.46, D.47, V.60, M.94, K.95, A.334, K.335 Ligand excluded by PLIP SO4.31: 6 residues within 4Å: Chain C: G.470, G.549, S.550, R.573, H.663, R.667 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain C: G.515, R.606, H.610 Ligand excluded by PLIP SO4.33: 5 residues within 4Å: Chain C: F.194, L.195, D.196, G.197, K.198 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain C: R.114, T.115 Ligand excluded by PLIP SO4.35: 11 residues within 4Å: Chain C: S.44, R.46, K.62, D.329, T.330, H.331, A.332, D.333, R.667, T.668 Ligands: GOL.37 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain C: T.437, Y.438, R.439 Ligand excluded by PLIP SO4.43: 6 residues within 4Å: Chain D: G.470, G.549, S.550, R.573, H.663, R.667 Ligand excluded by PLIP SO4.44: 4 residues within 4Å: Chain D: T.437, Y.438, R.439, K.535 Ligand excluded by PLIP SO4.45: 4 residues within 4Å: Chain D: L.195, D.196, G.197, K.198 Ligand excluded by PLIP SO4.46: 7 residues within 4Å: Chain D: R.46, D.47, V.60, M.94, K.95, A.334, K.335 Ligand excluded by PLIP SO4.47: 2 residues within 4Å: Chain D: R.355, R.357 Ligand excluded by PLIP

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

NA.9: 3 residues within 4Å: Chain A: D.243, P.244, D.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.245, A:D.245 Water bridges: A:D.245 NA.24: 5 residues within 4Å: Chain B: V.401, G.402, D.403, N.421, E.425 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.402, B:D.403, B:N.421 Water bridges: B:N.421 NA.25: 5 residues within 4Å: Chain B: E.219, E.220, E.221, A.238, N.239 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.219, B:E.220, B:E.221, B:N.239 NA.48: 5 residues within 4Å: Chain D: V.401, G.402, D.403, N.421, E.425 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.402, D:D.403, D:N.421 Water bridges: D:D.403, D:N.421

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 9 residues within 4Å: Chain A: L.39, L.42, K.62, I.64, Y.70, D.329, T.330, R.667, R.674 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.39, A:K.62, A:R.674, A:R.674 Water bridges: A:K.62, A:A.332 GOL.11: 8 residues within 4Å: Chain A: T.131, F.132, F.133, I.161, E.162, D.163, R.164, S.212 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.130, A:F.132, A:D.163, A:S.212, A:S.212 Water bridges: A:R.164 GOL.12: 7 residues within 4Å: Chain A: G.470, G.471, S.550, Y.551, F.591, R.633 Ligands: SO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.471, A:S.550, A:Y.551, A:R.633 GOL.13: 4 residues within 4Å: Chain A: W.318, Y.361, I.369, P.371 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.318 GOL.26: 4 residues within 4Å: Chain B: Q.35, G.36, T.37, L.486 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.35, B:G.36, B:T.37, B:T.37 Water bridges: B:S.490 GOL.27: 6 residues within 4Å: Chain B: T.131, F.132, F.133, I.161, R.164, S.212 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.132, B:F.132, B:S.212 GOL.28: 3 residues within 4Å: Chain B: D.432, M.451, K.452 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.452, B:K.452 GOL.37: 8 residues within 4Å: Chain C: L.39, L.42, S.44, K.62, I.64, Y.70, R.674 Ligands: SO4.35 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.39, C:R.674, C:R.674 Water bridges: C:I.64 GOL.38: 8 residues within 4Å: Chain C: T.131, F.132, F.133, I.161, E.162, D.163, R.164, S.212 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:F.132, C:E.162, C:R.164, C:S.212, C:S.212 GOL.39: 4 residues within 4Å: Chain C: Q.35, G.36, T.37, L.486 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.36, C:T.37, C:T.37 GOL.40: 2 residues within 4Å: Chain C: R.416, R.419 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.416, C:R.419, C:R.419 Water bridges: C:R.416 GOL.41: 3 residues within 4Å: Chain C: R.620, L.649, R.651 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.620, C:R.620, C:L.649, C:R.651 GOL.49: 9 residues within 4Å: Chain D: R.46, K.62, D.329, T.330, H.331, A.332, D.333, R.667, R.674 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.46, D:K.62, D:D.329, D:D.333, D:D.333, D:R.674, D:R.674 GOL.50: 2 residues within 4Å: Chain D: R.416, R.419 No protein-ligand interaction detected (PLIP)

4 x ALA: ALANINE(Non-covalent)

ALA.14: 8 residues within 4Å: Chain A: Q.572, R.573, L.626, H.627, S.628, F.658, L.665, R.677 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.572 Hydrogen bonds: A:R.677 Water bridges: A:R.573, A:S.628, A:H.663 ALA.29: 8 residues within 4Å: Chain B: Q.572, R.573, L.626, H.627, S.628, F.658, L.665, R.677 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.665 Hydrogen bonds: B:Q.572, B:R.573, B:R.677 Water bridges: B:S.628, B:S.628 ALA.42: 8 residues within 4Å: Chain C: Q.572, R.573, L.626, H.627, S.628, F.658, L.665, R.677 9 PLIP interactions: 7 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:Q.572 Hydrogen bonds: C:R.573, C:R.573, C:S.628, C:H.663, C:S.666, A.42 Water bridges: C:S.628, A.42 ALA.51: 9 residues within 4Å: Chain D: Q.572, R.573, L.626, H.627, S.628, F.658, L.665, S.666, R.677 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:L.626, D:F.658, D:R.677 Hydrogen bonds: D:R.573, D:L.626, D:S.666 Water bridges: D:S.628, D:H.663, D:L.665 Salt bridges: D:R.573, D:R.677

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chandravanshi, K. et al., Crystal structure and solution scattering of Geobacillus stearothermophilus S9 peptidase reveal structural adaptations for carboxypeptidase activity. Febs Lett. (2024)

Release Date

2024-03-13

Peptides

S9 family peptidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
G

S9 family peptidase

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