SMTL ID : 6vzq.4 (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: 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: RZP.2, MG.3, MG.4 16 PLIP interactions: 16 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:T.213, A:T.213, A:N.214, A:E.309 Water bridges: A:R.191, A:R.191 Salt bridges: A:K.75, A:K.75, A:K.124

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

RZP.2: 24 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.3, MG.4, GOL.11 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:A.129, A:N.311 Hydrogen bonds: A:G.128, A:R.130, A:R.169, A:R.169, A:Y.171, A:Y.171, A:N.214, A:Y.215, A:S.216, A:N.311, 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.3: 6 residues within 4Å: Chain A: D.296, E.309, N.311 Ligands: ADP.1, RZP.2, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.296, A:E.309, H2O.1 MG.4: 7 residues within 4Å: Chain A: G.128, A.129, E.309, N.311 Ligands: ADP.1, RZP.2, MG.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.309, A:E.309

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain A: K.244, Y.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.248 GOL.6: 3 residues within 4Å: Chain A: D.259, K.263, K.405 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.92, A:D.92, A:D.259, A:K.263 GOL.7: 8 residues within 4Å: Chain A: F.164, F.192, A.193, T.194, S.230, G.231, S.232, R.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.192, A:G.231, A:R.234 GOL.8: 4 residues within 4Å: Chain A: D.162, Y.242, H.246 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.162 GOL.9: 7 residues within 4Å: Chain A: I.160, I.161, D.162, G.163, Y.242 Ligands: GOL.8, GOL.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.162, A:Y.242, A:Y.242 GOL.10: 5 residues within 4Å: Chain A: N.240, E.251, W.254, R.255, R.395 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.240, A:R.255, A:R.395, A:R.395 GOL.11: 4 residues within 4Å: Chain A: R.18, D.46, Y.47 Ligands: RZP.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.18, A:R.18, A:S.313 GOL.12: 3 residues within 4Å: Chain A: L.153, I.155 Ligands: GOL.14 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.98, A:K.119 GOL.13: 4 residues within 4Å: Chain A: F.159, I.160, R.301 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.160, A:I.160, A:R.301 Water bridges: A:R.301 GOL.14: 4 residues within 4Å: Chain A: H.94, R.98, W.306 Ligands: GOL.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.94, A:K.304, A:K.304 Water bridges: A:R.98

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
D

Tubulin polyglutamylase TTLL6

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