SMTL ID : 6cd9.1

GID4 in complex with a peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x PRO- SER- ARG- TRP: Tetrapeptide PSRW(Non-covalent)

PRO-SER-ARG-TRP.1: 23 residues within 4Å: Chain A: Q.10, N.15, Y.17, L.37, I.39, G.41, L.42, E.115, G.129, A.130, S.131, F.132, Y.136, Y.151, H.153, S.155, S.156, Q.160 Ligands: UNX.11, UNX.16, UNX.25, UNX.26, UNX.47 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.39, A:L.42, A:F.132 Hydrogen bonds: A:Q.10, A:N.15, A:Y.17, A:G.41, A:G.129, A:S.131, A:S.131, A:Y.136, A:Y.136, A:S.156, A:S.156, A:Q.160 Water bridges: A:Y.17

46 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 3 residues within 4Å: Chain A: K.68, W.69, D.70 Ligand excluded by PLIP UNX.3: 4 residues within 4Å: Chain A: K.60, F.98, D.99, Y.100 Ligand excluded by PLIP UNX.4: 3 residues within 4Å: Chain A: S.31, S.59 Ligands: UNX.5 Ligand excluded by PLIP UNX.5: 4 residues within 4Å: Chain A: T.28, S.31, I.57 Ligands: UNX.4 Ligand excluded by PLIP UNX.6: 4 residues within 4Å: Chain A: L.103, K.104, Y.108, V.109 Ligand excluded by PLIP UNX.7: 2 residues within 4Å: Chain A: K.82, Y.159 Ligand excluded by PLIP UNX.8: 2 residues within 4Å: Chain A: K.78, W.158 Ligand excluded by PLIP UNX.9: 3 residues within 4Å: Chain A: H.25, D.27, Y.32 Ligand excluded by PLIP UNX.10: 3 residues within 4Å: Chain A: D.70, H.153, R.154 Ligand excluded by PLIP UNX.11: 3 residues within 4Å: Chain A: I.127 Ligands: PRO-SER-ARG-TRP.1, UNX.38 Ligand excluded by PLIP UNX.12: 2 residues within 4Å: Chain A: K.142, S.143 Ligand excluded by PLIP UNX.13: 2 residues within 4Å: Chain A: Y.36 Ligands: UNX.36 Ligand excluded by PLIP UNX.14: 4 residues within 4Å: Chain A: R.7, G.8, H.9, D.18 Ligand excluded by PLIP UNX.15: 4 residues within 4Å: Chain A: Y.17, D.18, K.40 Ligands: UNX.19 Ligand excluded by PLIP UNX.16: 5 residues within 4Å: Chain A: S.12, N.15, Y.17 Ligands: PRO-SER-ARG-TRP.1, UNX.26 Ligand excluded by PLIP UNX.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.18: 2 residues within 4Å: Chain A: S.12, N.15 Ligand excluded by PLIP UNX.19: 5 residues within 4Å: Chain A: H.9, S.16, Y.17, D.18 Ligands: UNX.15 Ligand excluded by PLIP UNX.20: 2 residues within 4Å: Chain A: T.43, E.44 Ligand excluded by PLIP UNX.21: 3 residues within 4Å: Chain A: Q.88, D.107, Y.108 Ligand excluded by PLIP UNX.22: 4 residues within 4Å: Chain A: K.114, E.115, F.132, A.133 Ligand excluded by PLIP UNX.23: 3 residues within 4Å: Chain A: A.144, T.165 Ligands: UNX.24 Ligand excluded by PLIP UNX.24: 5 residues within 4Å: Chain A: A.144, A.145, T.165, H.166 Ligands: UNX.23 Ligand excluded by PLIP UNX.25: 5 residues within 4Å: Chain A: S.131, Y.151, H.153, S.156 Ligands: PRO-SER-ARG-TRP.1 Ligand excluded by PLIP UNX.26: 5 residues within 4Å: Chain A: E.157, Q.160 Ligands: PRO-SER-ARG-TRP.1, UNX.16, UNX.47 Ligand excluded by PLIP UNX.27: 3 residues within 4Å: Chain A: E.157, W.158 Ligands: UNX.28 Ligand excluded by PLIP UNX.28: 3 residues within 4Å: Chain A: E.157, W.158 Ligands: UNX.27 Ligand excluded by PLIP UNX.29: 2 residues within 4Å: Chain A: E.148, N.163 Ligand excluded by PLIP UNX.30: 3 residues within 4Å: Chain A: N.15, S.16 Ligands: UNX.37 Ligand excluded by PLIP UNX.31: 2 residues within 4Å: Chain A: D.72, E.73 Ligand excluded by PLIP UNX.32: 3 residues within 4Å: Chain A: S.59, K.60, K.61 Ligand excluded by PLIP UNX.33: 2 residues within 4Å: Chain A: D.99, E.102 Ligand excluded by PLIP UNX.34: 3 residues within 4Å: Chain A: K.78, K.82 Ligands: UNX.35 Ligand excluded by PLIP UNX.35: 4 residues within 4Å: Chain A: K.78, K.82, Y.159 Ligands: UNX.34 Ligand excluded by PLIP UNX.36: 5 residues within 4Å: Chain A: E.20, V.22, Y.36, K.38 Ligands: UNX.13 Ligand excluded by PLIP UNX.37: 4 residues within 4Å: Chain A: N.15, S.16, Y.17 Ligands: UNX.30 Ligand excluded by PLIP UNX.38: 3 residues within 4Å: Chain A: I.127, S.128 Ligands: UNX.11 Ligand excluded by PLIP UNX.39: 6 residues within 4Å: Chain A: S.4, K.5, H.166, V.167 Ligands: UNX.40, UNX.41 Ligand excluded by PLIP UNX.40: 3 residues within 4Å: Chain A: S.4, H.166 Ligands: UNX.39 Ligand excluded by PLIP UNX.41: 2 residues within 4Å: Chain A: K.5 Ligands: UNX.39 Ligand excluded by PLIP UNX.42: 3 residues within 4Å: Chain A: L.49, T.50, V.119 Ligand excluded by PLIP UNX.43: 2 residues within 4Å: Chain A: D.74, K.78 Ligand excluded by PLIP UNX.44: 1 residues within 4Å: Chain A: D.126 Ligand excluded by PLIP UNX.45: 4 residues within 4Å: Chain A: F.93, S.95, F.98, Y.100 Ligand excluded by PLIP UNX.46: 4 residues within 4Å: Chain A: K.82, F.83, L.84, E.148 Ligand excluded by PLIP UNX.47: 5 residues within 4Å: Chain A: S.156, E.157 Ligands: PRO-SER-ARG-TRP.1, PRO-SER-ARG-TRP.1, UNX.26 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, C. et al., Molecular basis of GID4-mediated recognition of degrons for the Pro/N-end rule pathway. Nat. Chem. Biol. (2018)

Release Date

2018-03-07

Peptides

Glucose-induced degradation protein 4 homolog: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glucose-induced degradation protein 4 homolog

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