SMTL ID : 8wt1.1 (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

36 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: 7 residues within 4Å: Chain A: G.470, G.549, S.550, R.573, H.663, R.667 Ligands: NA.12 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: R.355, R.357 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: T.437, Y.438, R.439, K.535 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: L.195, D.196, G.197, K.198 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: H.609, K.614 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: R.416, R.419 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: S.63, H.73, Q.85 Ligand excluded by PLIP SO4.18: 8 residues within 4Å: Chain B: R.46, D.47, V.60, M.94, K.95, D.333, A.334, K.335 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain B: H.609, K.614 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain B: L.195, D.196, G.197, K.198 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain B: G.515, R.606 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain B: G.470, G.549, S.550, R.573, H.663, R.667 Ligand excluded by PLIP SO4.23: 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 SO4.24: 3 residues within 4Å: Chain B: K.283, R.312, L.365 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain B: R.416, R.419 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain B: R.355, R.357 Ligands: NA.30 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: Y.438, R.439, K.535 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain B: H.49, R.97, K.335, P.337 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain B: R.620, L.649, R.651 Ligand excluded by PLIP SO4.37: 7 residues within 4Å: Chain C: R.46, D.47, V.60, M.94, K.95, A.334, K.335 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain C: E.602, D.603, A.604, E.605 Ligand excluded by PLIP SO4.39: 6 residues within 4Å: Chain C: G.470, G.549, S.550, R.573, H.663, R.667 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain C: E.388, Q.389, Q.390 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain C: T.437, Y.438, R.439, K.535 Ligand excluded by PLIP SO4.42: 2 residues within 4Å: Chain C: R.355, R.357 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain C: L.195, D.196, G.197, K.198 Ligand excluded by PLIP SO4.50: 7 residues within 4Å: Chain D: R.46, D.47, V.60, M.94, K.95, A.334, K.335 Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain D: G.515, R.606, H.610 Ligand excluded by PLIP SO4.52: 6 residues within 4Å: Chain D: G.470, G.549, S.550, R.573, H.663, R.667 Ligand excluded by PLIP SO4.53: 2 residues within 4Å: Chain D: R.355, R.357 Ligand excluded by PLIP SO4.54: 4 residues within 4Å: Chain D: E.602, D.603, A.604, E.605 Ligand excluded by PLIP SO4.55: 5 residues within 4Å: Chain D: T.437, Y.438, R.439, A.531, K.535 Ligand excluded by PLIP SO4.56: 4 residues within 4Å: Chain D: L.195, D.196, G.197, K.198 Ligand excluded by PLIP SO4.57: 2 residues within 4Å: Chain D: R.416, R.419 Ligand excluded by PLIP SO4.58: 3 residues within 4Å: Chain D: H.73, Q.85, F.88 Ligand excluded by PLIP

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

NA.9: 6 residues within 4Å: Chain A: S.628, D.631, N.662, H.663, L.665 Ligands: ALA.16 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: A.16, A:S.628, A:H.663 NA.10: 6 residues within 4Å: Chain A: S.400, V.401, G.402, D.403, N.421, E.425 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.402, A:D.403, A:N.421 Water bridges: A:N.421 NA.11: 3 residues within 4Å: Chain A: G.515, R.606, H.610 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.515, A:R.606 NA.12: 5 residues within 4Å: Chain A: G.470, G.471, S.550, Y.551 Ligands: SO4.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.471, A:G.471, A:Y.551 Water bridges: A:S.550 NA.30: 5 residues within 4Å: Chain B: R.355, R.357, Q.447, F.478 Ligands: SO4.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.447, B:Q.447 Water bridges: B:N.376 NA.31: 7 residues within 4Å: Chain B: V.560, T.563, D.564, H.618, M.619, R.620, T.621 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.620, B:T.621, B:T.621 Water bridges: B:T.621 NA.32: 3 residues within 4Å: Chain B: S.582, D.599, V.600 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.582, B:D.599, B:V.600 NA.33: 7 residues within 4Å: Chain B: S.109, D.110, R.111, S.112, R.114, Q.116, W.118 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.112, B:S.112, B:Q.116 NA.44: 5 residues within 4Å: Chain C: V.401, G.402, D.403, N.421, E.425 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.402, C:D.403, C:N.421, C:N.421 Water bridges: C:D.403 NA.59: 6 residues within 4Å: Chain D: D.403, R.419, A.420, N.421, E.422, E.425 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.403, D:N.421 Water bridges: D:R.416, D:N.421

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain A: S.224, A.273, S.274 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.274, A:S.274 Water bridges: A:D.139, A:F.225, A:S.274 GOL.14: 7 residues within 4Å: Chain A: T.131, F.132, F.133, I.161, E.162, R.164, S.212 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.132, A:F.133, A:I.161, A:E.162, A:R.164, A:S.212 GOL.15: 4 residues within 4Å: Chain A: W.318, Y.361, I.369, P.371 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.369 GOL.34: 9 residues within 4Å: Chain B: L.130, T.131, F.132, F.133, I.161, E.162, D.163, R.164, S.212 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.130, B:F.132, B:E.162, B:S.212 GOL.35: 6 residues within 4Å: Chain B: Y.186, E.221, D.245, R.250, Y.589, F.590 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.221, B:D.245, B:R.250 Water bridges: B:N.239, B:R.250 GOL.45: 7 residues within 4Å: Chain C: L.39, L.42, K.62, S.63, I.64, Y.70, R.674 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.674, C:R.674 GOL.46: 2 residues within 4Å: Chain C: R.101, E.103 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.101 Water bridges: C:E.103 GOL.47: 2 residues within 4Å: Chain C: R.416, R.419 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.416, C:R.419, C:R.419 GOL.48: 7 residues within 4Å: Chain C: T.131, F.132, F.133, I.161, E.162, D.163, S.212 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:F.132, C:F.132, C:S.212 Water bridges: C:L.130, C:S.212 GOL.60: 4 residues within 4Å: Chain D: Q.35, G.36, T.37, L.486 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.36, D:T.37, D:T.37

4 x ALA: ALANINE(Non-covalent)

ALA.16: 9 residues within 4Å: Chain A: Q.572, R.573, L.626, H.627, S.628, F.658, L.665, R.677 Ligands: NA.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.665 Hydrogen bonds: A:Q.572, A:R.573, A:R.573, A:S.628 Water bridges: A:S.628, A:S.666 ALA.36: 9 residues within 4Å: Chain B: Q.572, R.573, L.626, H.627, S.628, F.658, L.665, S.666, R.677 7 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain B Water bridges: A.36, B:R.573, B:S.628, B:H.663 Hydrophobic interactions: B:Q.572 Hydrogen bonds: B:R.573, B:S.666 ALA.49: 8 residues within 4Å: Chain C: Q.572, R.573, L.626, H.627, S.628, F.658, L.665, R.677 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.658, C:L.665 Hydrogen bonds: C:Q.572, C:R.677 Water bridges: C:S.666, C:S.666 Salt bridges: C:R.573, C:R.677 ALA.61: 8 residues within 4Å: Chain D: Q.572, R.573, L.626, H.627, 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:L.665, D:R.677 Hydrogen bonds: D:Q.572, D:R.573, D:L.626, D:S.666 Water bridges: D:S.628 Salt bridges: D:R.573, D:R.677

2 x FLC: CITRATE ANION(Non-covalent)

FLC.17: 13 residues within 4Å: Chain A: L.42, S.44, R.46, K.62, I.64, Y.70, D.329, T.330, H.331, A.332, D.333, R.667, R.674 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.62, A:D.329, A:H.331, A:A.332, A:D.333, A:R.667 Salt bridges: A:R.46, A:K.62, A:K.62, A:R.674 FLC.62: 14 residues within 4Å: Chain D: L.39, L.42, S.44, R.46, K.62, S.63, I.64, Y.70, D.329, T.330, H.331, A.332, R.667, R.674 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.44, D:S.44, D:K.62, D:K.62, D:Y.70, D:H.331, D:A.332 Salt bridges: D:R.46, D:K.62, D:R.674

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
A

B
B

C
C

D
H

S9 family peptidase

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