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

TTLL6 bound to the initiation analog

Coordinates

PDB Format Compare

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.10, MG.11, MG.12 19 PLIP interactions: 19 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:K.75, A:G.128, A:R.191 Salt bridges: A:R.169, A:R.191, A:R.191, A:K.233, A:K.327

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: D.249, E.251, Q.252, R.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.249, A:R.255 GOL.3: 3 residues within 4Å: Chain A: D.92, D.259, K.263 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.263 GOL.4: 4 residues within 4Å: Chain A: R.18, Y.19, D.20, S.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.20, A:D.20, A:S.317 GOL.5: 4 residues within 4Å: Chain A: I.160, I.161, D.162, G.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.160, A:D.162, A:G.163 GOL.6: 2 residues within 4Å: Chain A: Q.28, Y.332 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.28 GOL.7: 1 residues within 4Å: Chain A: R.301 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.301 GOL.8: 1 residues within 4Å: Chain A: E.325 No protein-ligand interaction detected (PLIP) GOL.9: 2 residues within 4Å: Chain A: Q.28, Y.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.29

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

ADP.10: 26 residues within 4Å: Chain A: K.75, P.97, I.122, K.124, C.129, Q.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.11, MG.12 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.11: 5 residues within 4Å: Chain A: E.309, N.311 Ligands: 2TI.1, ADP.10, MG.12 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.309, A:E.309, H2O.1 MG.12: 6 residues within 4Å: Chain A: N.214, D.296, E.309 Ligands: 2TI.1, ADP.10, MG.11 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
B

Tubulin polyglutamylase TTLL6

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