SMTL ID : 6lvs.2 (5 other biounits)

USP14 catalytic domain mutant C114S

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: G.36, N.37, T.38, Y.40, H.105, F.111, E.113, Y.120, L.121, Q.122 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.36, A:H.105, A:L.121, A:Q.123 GOL.2: 4 residues within 4Å: Chain A: Q.343, G.350, H.351, H.389 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.389 GOL.3: 8 residues within 4Å: Chain A: F.247, F.248, Y.249, N.256, A.257, S.346, S.347 Ligands: NA.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.124, A:D.124, A:F.248, A:A.257, A:S.347, A:S.347

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

NA.4: 6 residues within 4Å: Chain A: T.33, L.35, T.38, M.41, N.42, P.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.35, A:N.42, A:N.42 NA.5: 6 residues within 4Å: Chain A: M.244, R.246, V.263, F.265, S.383, A.391 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.246, A:V.263 NA.6: 6 residues within 4Å: Chain A: N.37, S.39, G.350, H.351 Ligands: FMT.12, FMT.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.37, A:S.39 Water bridges: A:Y.40 NA.7: 7 residues within 4Å: Chain A: S.39, N.42, A.43, Y.352, F.366, D.368 Ligands: FMT.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.39, A:A.43, A:D.368 NA.8: 6 residues within 4Å: Chain A: F.163, L.189, Y.239, L.240, T.241 Ligands: FMT.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.239, A:T.241, A:T.241 NA.9: 4 residues within 4Å: Chain A: N.256, S.347, S.348 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.347, A:S.348 NA.10: 5 residues within 4Å: Chain A: R.209, L.210, E.212, K.229, S.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.229, A:S.231 NA.11: 3 residues within 4Å: Chain A: Q.110, E.127, Q.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.127, A:Q.131 Water bridges: A:Q.110

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

FMT.12: 10 residues within 4Å: Chain A: N.34, N.37, T.38, S.39, Q.122, G.350, H.351 Ligands: NA.6, FMT.15, BME.20 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.34, A:N.37, A:S.39, A:S.39, A:H.351 FMT.13: 7 residues within 4Å: Chain A: W.129, M.133, F.163, L.189, Q.190, T.241 Ligands: NA.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.190 FMT.14: 8 residues within 4Å: Chain A: L.32, N.42, A.43, Q.46, S.354, F.366, D.368 Ligands: NA.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.32, A:Q.46, A:D.368 FMT.15: 9 residues within 4Å: Chain A: S.39, Q.122, S.347, S.349, G.350, H.351, Y.352 Ligands: NA.6, FMT.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.342 Water bridges: A:Q.123 FMT.16: 5 residues within 4Å: Chain A: K.55, L.58, K.59, F.85, D.89 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.55, A:K.59 Water bridges: A:D.86, A:D.86 FMT.17: 5 residues within 4Å: Chain A: R.49, S.50, V.51, P.52, K.55 No protein-ligand interaction detected (PLIP) FMT.18: 5 residues within 4Å: Chain A: Y.201, L.202, F.203, K.264, P.266 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.203

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.19: 3 residues within 4Å: Chain A: L.35, G.36, Q.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.34 BME.20: 3 residues within 4Å: Chain A: N.34, N.37 Ligands: FMT.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, H.C., USP14 catalytic domain mutant C114S. To Be Published

Release Date

2020-03-18

Peptides

Ubiquitin carboxyl-terminal hydrolase 14: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Ubiquitin carboxyl-terminal hydrolase 14

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