SMTL ID : 6vzs.1 (3 other biounits)

Engineered TTLL6 mutant bound to gamma-elongation analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

monomer

Ligands

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

ADP.1: 25 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, H.211, L.212, T.213, N.214, D.296, L.298, L.308, E.309 Ligands: S3A.2, MG.13, MG.14 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.124, A:G.128, 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 Water bridges: A:K.75, A:K.75, A:R.191 Salt bridges: A:K.75, A:K.75, A:K.124

1 x S3A: (2~{S})-2-[[[(3~{R})-3-acetamido-4-oxidanyl-4-oxidanylidene-butyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid(Non-covalent)

S3A.2: 23 residues within 4Å: Chain A: Y.19, A.129, R.130, R.169, Y.171, L.189, R.191, N.214, Y.215, S.216, K.233, D.296, E.309, N.311, I.312, S.313, P.314, S.315, D.323, K.327 Ligands: ADP.1, MG.13, MG.14 21 PLIP interactions: 21 interactions with chain A 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.313, A:S.315 Water bridges: A:K.75, A:R.191, A:I.312, A:I.312 Salt bridges: A:R.169, A:R.191, A:R.191, A:K.233, A:K.327

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: C.209, S.221 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.195, A:N.223 GOL.4: 4 residues within 4Å: Chain A: P.97, R.98, L.153, W.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.98 Water bridges: A:K.119 GOL.5: 6 residues within 4Å: Chain A: R.18, Y.19, D.20, S.317, T.318, D.319 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.18, A:D.20, A:S.317, A:T.318, A:T.318, A:T.318, A:D.319 Water bridges: A:S.21 GOL.6: 3 residues within 4Å: Chain A: S.216, K.219, H.220 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.216, A:K.219 Water bridges: A:R.130, A:K.219 GOL.7: 5 residues within 4Å: Chain A: N.240, E.251, W.254, R.255, R.395 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.240, A:R.255, A:R.395 Water bridges: A:N.186, A:N.186, A:R.395 GOL.8: 4 residues within 4Å: Chain A: P.125, G.133, D.148, M.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.148 Water bridges: A:D.148 GOL.9: 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:A.193, A:S.230, A:R.234 GOL.10: 1 residues within 4Å: Chain A: R.301 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.301 GOL.11: 5 residues within 4Å: Chain A: D.259, K.263, K.405, Y.406, F.409 No protein-ligand interaction detected (PLIP) GOL.12: 2 residues within 4Å: Chain A: E.187, S.237 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.235

2 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 6 residues within 4Å: Chain A: N.214, D.296, E.309 Ligands: ADP.1, S3A.2, MG.14 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.296, A:E.309, H2O.1 MG.14: 5 residues within 4Å: Chain A: E.309, N.311 Ligands: ADP.1, S3A.2, MG.13 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.309, 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
A

Tubulin polyglutamylase TTLL6

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