SMTL ID : 6vzr.1 (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: 27 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, GOL.5, MG.10, MG.11 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:R.130, A:R.130, A:R.169, A:R.169, A:Y.171, A:N.214, A:Y.215, A:S.216, A:E.309, A:S.313, A:S.313, A:S.315 Water bridges: A:R.18, A:K.75, A:R.191, A:R.191 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: 27 residues within 4Å: Chain A: K.75, P.97, 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.10, MG.11 19 PLIP interactions: 19 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:D.296, A:E.309 Water bridges: A:K.75, A:R.191, A:R.191 Salt bridges: A:K.75, A:K.75, A:K.124

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: D.92, D.259, K.263, K.405, Y.406 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.92, A:D.92, A:K.263 GOL.4: 6 residues within 4Å: Chain A: R.18, Y.19, D.20, S.317, T.318, D.319 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.20, A:D.20, A:T.318, A:T.318 Water bridges: A:S.21, A:R.24 GOL.5: 9 residues within 4Å: Chain A: R.130, Y.215, K.233, S.315, S.317, D.319, D.323, K.327 Ligands: 2TI.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.130, A:K.233, A:S.315, A:S.317, A:D.319, A:D.323, A:K.327, A:K.327 Water bridges: A:S.315, A:S.317 GOL.6: 6 residues within 4Å: Chain A: Y.215, F.224, Q.226, K.233, S.320, D.323 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.233, A:K.233, A:S.320 GOL.7: 7 residues within 4Å: Chain A: Y.185, N.186, E.187, K.235, E.325, V.326, S.329 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.187, A:K.235, A:K.235, A:S.329 Water bridges: A:Y.185, A:Y.185 GOL.8: 6 residues within 4Å: Chain A: K.119, L.153, Y.154, I.155, S.156, W.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.156 Water bridges: A:S.156 GOL.9: 6 residues within 4Å: Chain A: P.179, L.180, H.269, K.273, Y.398, F.410 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.180, A:Y.398, A:Y.398 Water bridges: A:D.407 GOL.12: 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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain A: E.309, N.311 Ligands: 2TI.1, ADP.2, MG.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.309, A:E.309, H2O.2 MG.11: 6 residues within 4Å: Chain A: N.214, D.296, E.309 Ligands: 2TI.1, ADP.2, 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
TTLL6 unregistered chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

Tubulin polyglutamylase TTLL6

TTLL6 unregistered chain

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