SMTL ID : 6vzw.4 (3 other biounits)

TTLL6 bound to the initiation analog

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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: 25 residues within 4Å: Chain A: Y.19, C.73, C.129, Q.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, H.312, S.313, P.314, S.315, D.323, K.327 Ligands: ADP.9, MG.10, MG.11 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:N.311 Hydrogen bonds: A:Q.130, A:R.169, A:R.169, A:N.214, A:Y.215, A:S.216, A:N.311, A:S.313, A:S.313, A:S.315 Water bridges: A:G.128, A:Y.171, A:R.191, A:N.311, A:S.315 Salt bridges: A:R.169, A:R.191, A:R.191, A:K.233, A:K.327

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: D.46, Y.47, S.48, H.312 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.46, A:S.48, A:S.48 GOL.3: 10 residues within 4Å: Chain A: F.164, F.192, A.193, T.194, N.223, V.225, S.230, G.231, S.232, R.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.223, A:S.230, A:R.234 GOL.4: 5 residues within 4Å: Chain A: N.240, V.250, E.251, W.254, R.395 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.255, A:R.395 Water bridges: A:N.240 GOL.5: 4 residues within 4Å: Chain A: D.249, E.251, Q.252, R.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.249 GOL.6: 6 residues within 4Å: Chain A: R.18, Y.19, D.20, S.317, T.318, D.319 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.20, A:D.20, A:T.318, A:T.318 Water bridges: A:S.21 GOL.7: 2 residues within 4Å: Chain A: N.16, Y.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.47 GOL.8: 1 residues within 4Å: Chain A: Q.252 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.252

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

ADP.9: 26 residues within 4Å: Chain A: K.75, P.97, I.122, K.124, G.128, C.129, Q.130, G.131, I.134, Q.152, L.153, Y.154, I.155, K.165, D.167, H.211, L.212, T.213, N.214, D.296, L.298, L.308, E.309 Ligands: 2TI.1, MG.10, MG.11 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.124, A:G.128, A:C.129, A:Q.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 Water bridges: A:R.191, A:R.191 Salt bridges: A:K.75, A:K.75, A:K.124

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 6 residues within 4Å: Chain A: K.75, E.309, N.311 Ligands: 2TI.1, ADP.9, MG.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.309, A:E.309, H2O.1 MG.11: 7 residues within 4Å: Chain A: R.191, N.214, D.296, E.309 Ligands: 2TI.1, ADP.9, MG.10 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.296, A:E.309, H2O.2

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
D

Tubulin polyglutamylase TTLL6

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