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

Engineered TTLL6 mutant bound to alpha-elongation analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.08 Å

Oligo State

monomer

Ligands

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

ADP.1: 26 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, H.211, L.212, T.213, N.214, D.296, L.298, L.308, E.309 Ligands: RZP.4, MG.5, MG.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.124, A:A.129, A:G.131, A:Q.152, A:I.155, A:K.165, A:D.167, A:T.213, A:T.213, A:N.214 Salt bridges: A:K.75, A:K.75, A:K.124

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.18, Y.19, D.20, S.317, T.318 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.20, A:S.317, A:T.318, A:T.318 GOL.3: 7 residues within 4Å: Chain A: K.119, L.153, Y.154, I.155, S.156, W.306 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.156 Water bridges: A:K.119 GOL.7: 4 residues within 4Å: Chain A: R.18, Y.47, S.313 Ligands: RZP.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.313 GOL.8: 4 residues within 4Å: Chain A: H.94, F.96, R.98 Ligands: GOL.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.94, A:R.98, A:K.304 Water bridges: A:R.98, A:K.304 GOL.9: 8 residues within 4Å: Chain A: V.184, Y.185, N.186, L.236, N.240, W.254, R.395 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.186, A:N.240, A:R.395, A:R.395 GOL.10: 5 residues within 4Å: Chain A: K.244, E.251, W.254, R.255 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.244, A:K.244, A:R.255, A:R.255 GOL.11: 9 residues within 4Å: Chain A: F.164, F.192, A.193, T.194, N.223, S.230, G.231, S.232, R.234 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.193, A:N.223, A:S.230, A:R.234

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

RZP.4: 24 residues within 4Å: Chain A: Y.19, G.128, A.129, R.130, R.169, 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.5, MG.6, GOL.7 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:A.129, A:N.311 Hydrogen bonds: A:R.130, A:R.130, A:R.169, A:R.169, A:N.214, A:Y.215, A:S.216, A:S.216, A:I.312, A:S.313, A:S.313, A:S.315 Salt bridges: A:R.169, A:R.191, A:R.191, A:K.233, A:K.327

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain A: R.191, N.214, D.296, E.309 Ligands: ADP.1, RZP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.296 MG.6: 6 residues within 4Å: Chain A: K.75, A.129, E.309, N.311 Ligands: ADP.1, RZP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.309, 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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Tubulin polyglutamylase TTLL6

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