SMTL ID : 6vzr.3 (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, 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.8, MG.9 23 PLIP interactions: 23 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:K.75, A:R.191, A:R.191, A:K.233, A:K.233, A:N.311 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.8, MG.9 20 PLIP interactions: 20 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:K.75, A:R.191, A:R.191 Salt bridges: A:K.75, A:K.75, A:K.124

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: R.9, Q.27, L.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.9, A:L.31 GOL.4: 4 residues within 4Å: Chain A: E.251, W.254, R.255, R.395 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.255, A:R.255 Water bridges: A:N.186, A:W.254 GOL.5: 4 residues within 4Å: Chain A: S.241, Y.242, T.245, H.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.241, A:S.241 GOL.6: 3 residues within 4Å: Chain A: Q.28, D.328, S.329 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.28, A:Q.28, A:D.328 GOL.7: 7 residues within 4Å: Chain A: S.156, K.157, P.158, I.160, Y.197, H.199, R.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.158, A:H.199 GOL.10: 5 residues within 4Å: Chain A: R.18, Y.19, D.20, S.317, T.318 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.18, A:D.20, A:T.318, A:T.318 Water bridges: A:S.21 GOL.11: 4 residues within 4Å: Chain A: L.153, Y.154, I.155, W.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.154 Water bridges: A:S.156, A:S.156 GOL.12: 3 residues within 4Å: Chain A: D.162, Y.242, H.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.162, A:H.246 GOL.13: 6 residues within 4Å: Chain A: F.183, E.387, K.388, C.391, R.395, L.396 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.387, A:L.396

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 7 residues within 4Å: Chain A: R.191, N.214, D.296, E.309 Ligands: 2TI.1, ADP.2, MG.9 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.296, A:E.309, H2O.2 MG.9: 7 residues within 4Å: Chain A: K.75, A.129, E.309, N.311 Ligands: 2TI.1, ADP.2, MG.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.309, A:E.309, H2O.1

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
C

Tubulin polyglutamylase TTLL6

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