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

Engineered TTLL6 bound to the initiation analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

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, C.73, 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.4, MG.5 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:A.129 Hydrogen bonds: A:R.130, A:R.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:R.18, A:K.75, A:G.128 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, P.97, I.122, K.124, 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.4, MG.5 18 PLIP interactions: 18 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, A:N.311 Water bridges: A:K.75, A:K.75 Salt bridges: A:K.75, A:K.75, A:K.124

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: R.18, Y.19, D.20, S.317, T.318 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.18, A:D.20, A:T.318, A:T.318 Water bridges: A:S.21, A:R.24 GOL.6: 4 residues within 4Å: Chain A: N.240, E.251, R.255, R.395 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.240, A:R.255, A:R.255, A:R.395, A:R.395

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: E.309, N.311 Ligands: 2TI.1, ADP.2, MG.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.309, A:E.309, H2O.1 MG.5: 7 residues within 4Å: Chain A: R.191, N.214, D.296, E.309 Ligands: 2TI.1, ADP.2, MG.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.296, 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
TTLL6 unregistered chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
F

Tubulin polyglutamylase TTLL6

TTLL6 unregistered chain

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