SMTL ID : 6i44.1

Allosteric activation of human prekallikrein by apple domain disc rotation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.116, N.133 Ligands: FMT.14 No protein-ligand interaction detected (PLIP)

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.2: 11 residues within 4Å: Chain A: D.561, A.562, C.563, K.564, T.585, S.586, W.587, G.588, G.590, C.591, G.598 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.585 Hydrogen bonds: A:D.561 Water bridges: A:W.587, A:W.587, A:E.589

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 8 residues within 4Å: Chain A: M.38, R.39, F.42, A.99, P.182, Y.222, P.224 Ligands: FMT.21 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.42, A:A.99, A:P.182 Water bridges: A:Y.35

1 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.4: 9 residues within 4Å: Chain A: Y.15, E.16, A.18, F.20, T.75, L.76, K.78, V.79, H.80 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.20, A:T.75 Hydrogen bonds: A:K.78

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

SO4.5: 2 residues within 4Å: Chain A: Y.222 Ligands: FMT.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.280

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

CL.6: 1 residues within 4Å: Ligands: NA.7 Ligand excluded by PLIP

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

NA.7: 4 residues within 4Å: Chain A: T.218, C.281, H.282 Ligands: CL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.218, A:C.281, A:H.282 Water bridges: A:S.283

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 5 residues within 4Å: Chain A: S.467, E.468, G.469, Y.544, W.587 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.469, A:G.469, A:N.470, A:N.470 PEG.9: 7 residues within 4Å: Chain A: G.23, D.24, V.25, D.70, V.72, R.316 Ligands: FMT.15 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.70

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain A: L.325, D.328, K.335, F.337 Ligands: ACT.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.335 Water bridges: A:K.335 GOL.11: 2 residues within 4Å: Chain A: F.19, R.81 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.81 GOL.12: 6 residues within 4Å: Chain A: S.27, M.28, Y.29, E.61, K.62, F.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.27, A:S.27 GOL.13: 7 residues within 4Å: Chain A: D.109, S.140, A.142, F.146, Y.151, L.156, K.158 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.158, A:K.158 Water bridges: A:R.111, A:N.114

8 x FMT: FORMIC ACID(Non-functional Binders)

FMT.14: 4 residues within 4Å: Chain A: K.128, R.129, N.132 Ligands: NAG-NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.132 FMT.15: 4 residues within 4Å: Chain A: V.72, E.294, R.316 Ligands: PEG.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.316, A:R.316 Water bridges: A:E.294 FMT.16: 3 residues within 4Å: Chain A: E.557, G.558, K.560 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.557 FMT.17: 5 residues within 4Å: Chain A: I.219, H.282, G.344, Y.359 Ligands: SO4.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.282 FMT.18: 4 residues within 4Å: Chain A: G.94, C.364, N.365, T.366 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.366 Water bridges: A:G.94, A:G.94, A:H.95 FMT.19: 5 residues within 4Å: Chain A: G.389, E.390, P.392, W.393, W.579 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.489, A:K.489, A:K.489 FMT.20: 2 residues within 4Å: Chain A: R.362, L.363 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.362 Water bridges: A:F.42, A:L.363 FMT.21: 7 residues within 4Å: Chain A: C.220, T.221, H.223, C.226, S.269, L.271 Ligands: MPD.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.223, A:S.269

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.22: 3 residues within 4Å: Chain A: Y.159, E.251 Ligands: ACT.25 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.159 ACT.23: 5 residues within 4Å: Chain A: D.290, F.337, R.339, R.348 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.337 Hydrogen bonds: A:R.348 Water bridges: A:S.323 Salt bridges: A:R.339 ACT.24: 3 residues within 4Å: Chain A: A.199, F.200, S.201 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.232, A:Y.232, A:Q.261 ACT.25: 7 residues within 4Å: Chain A: R.135, Y.159, L.227, T.249, S.250, E.251 Ligands: ACT.22 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.135, A:L.227 Hydrogen bonds: A:E.251 Water bridges: A:R.135, A:T.249 ACT.26: 4 residues within 4Å: Chain A: V.72, G.74, I.315, R.316 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.315 Water bridges: A:R.316 ACT.27: 3 residues within 4Å: Chain A: E.390, W.391, W.579 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.579 Salt bridges: A:K.526

1 x GLY: GLYCINE(Non-covalent)

GLY.28: 5 residues within 4Å: Chain A: T.12, L.14, Q.34, Q.37, N.576 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.12, A:Q.34, A:Q.37

1 x SER: SERINE(Non-covalent)

SER.29: 5 residues within 4Å: Chain A: F.214, R.217, T.218, L.270, P.278 7 PLIP interactions: 5 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:R.217, A:T.218, S.29, S.29 Water bridges: A:T.218, A:T.218 Salt bridges: A:R.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, C. et al., Plasma kallikrein structure reveals apple domain disc rotated conformation compared to factor XI. J.Thromb.Haemost. (2019)

Release Date

2019-03-06

Peptides

Plasma kallikrein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Plasma kallikrein