SMTL ID : 8v3n.1

CCP5 in complex with Glu-P-Glu transition state analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.252, E.255, H.353 Ligands: 01.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.252, A:E.255, A:E.255, A:H.353

2 x MLT: D-MALATE(Non-covalent)

MLT.2: 7 residues within 4Å: Chain A: R.271, R.276, A.457, S.458, Q.476, R.479, R.496 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:S.458 Hydrogen bonds: A:S.458, A:Q.476 Water bridges: A:R.276 Salt bridges: A:R.271, A:R.276, A:R.276, A:R.479, A:R.496 MLT.3: 4 residues within 4Å: Chain A: G.70, R.72, N.96, K.97 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.72, A:R.72, A:N.96, A:K.97 Salt bridges: A:R.72, A:R.72, A:K.97

1 x 01: (2S)-2-{[(S)-[(3S)-3-acetamido-4-(ethylamino)-4-oxobutyl](hydroxy)phosphoryl]methyl}pentanedioic acid

01.4: 18 residues within 4Å: Chain A: Q.98, H.252, E.255, Y.302, R.303, N.312, R.313, H.353, G.354, H.355, A.356, S.357, Y.364, K.414, S.417, R.419, T.433 Ligands: ZN.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.302, A:Y.364, A:T.433 Hydrogen bonds: A:R.303, A:R.303, A:N.312, A:A.356, A:N.402, A:S.417, A:T.433 Water bridges: A:R.419 Salt bridges: A:H.252, A:R.303, A:R.313, A:H.353, A:K.414, A:K.414, A:R.419

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, J. et al., Tubulin code eraser CCP5 binds branch glutamates by substrate deformation. Nature (2024)

Release Date

2024-07-17

Peptides

Cytosolic carboxypeptidase-like protein 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytosolic carboxypeptidase-like protein 5

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