SMTL ID : 6vzr.2 (3 other biounits)

Engineered TTLL6 bound to the initiation analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x 2TI: (2~{S})-2-[[[(3~{R})-3-acetamido-4-(ethylamino)-4-oxidanylidene-butyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid(Non-covalent)

2TI.1: 26 residues within 4Å: Chain A: R.18, Y.19, G.128, A.129, R.130, R.169, Y.171, L.189, R.191, N.214, Y.215, S.216, K.233, D.296, E.309, V.310, N.311, I.312, S.313, P.314, S.315, D.323, K.327 Ligands: ADP.2, MG.6, MG.7 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.312 Hydrogen bonds: A:G.128, A:R.130, A:R.130, A:R.169, A:R.169, A:N.214, A:Y.215, A:S.216, A:S.216, A:N.311, A:I.312, A:S.313, A:S.313, A:S.315 Water bridges: A:R.18 Salt bridges: A:R.169, A:R.191, A:R.191, A:K.233, A:K.327

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 26 residues within 4Å: Chain A: K.75, I.122, K.124, G.128, A.129, R.130, G.131, I.134, Q.152, L.153, Y.154, I.155, K.165, D.167, R.191, H.211, L.212, T.213, N.214, D.296, L.298, L.308, E.309 Ligands: 2TI.1, MG.6, MG.7 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.124, A:A.129, A:R.130, A:G.131, A:Q.152, A:I.155, A:K.165, A:D.167, A:T.213, A:N.214, A:N.214, A:L.308 Salt bridges: A:K.75, A:K.75, A:K.124

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: R.9, Q.27, G.30, L.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.27, A:L.31 Water bridges: A:R.9 GOL.4: 6 residues within 4Å: Chain A: N.240, E.251, W.254, R.255, R.395 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.240, A:E.251, A:R.255, A:R.255, A:R.395 GOL.5: 6 residues within 4Å: Chain A: S.237, N.240, S.241, K.244, E.251 Ligands: GOL.4 No protein-ligand interaction detected (PLIP) GOL.8: 3 residues within 4Å: Chain A: K.119 Ligands: GOL.9, GOL.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.119, A:K.119 GOL.9: 3 residues within 4Å: Chain A: R.98, Y.112 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.98 GOL.10: 6 residues within 4Å: Chain A: L.153, Y.154, I.155, S.156, W.306 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.156, A:S.156 Water bridges: A:K.157 GOL.11: 5 residues within 4Å: Chain A: Y.215, F.224, Q.226, D.319, S.320 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.215 Water bridges: A:S.320, A:D.323

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 6 residues within 4Å: Chain A: R.191, N.214, D.296, E.309 Ligands: 2TI.1, ADP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.296 MG.7: 6 residues within 4Å: Chain A: G.128, A.129, E.309, N.311 Ligands: 2TI.1, ADP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.309, A:E.309

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mahalingan, K.K. et al., Structural basis for polyglutamate chain initiation and elongation by TTLL family enzymes. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-08-12

Peptides

Tubulin polyglutamylase TTLL6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Tubulin polyglutamylase TTLL6

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