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

Engineered TTLL6 mutant bound to gamma-elongation analog

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

monomer

Ligands

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: T.137, S.139, E.142, D.206 Ligand excluded by PLIP GOL.4: 8 residues within 4Å: Chain A: C.73, R.74, S.127, G.128, E.309, V.310, I.312 Ligands: S3A.3 Ligand excluded by PLIP GOL.5: 2 residues within 4Å: Chain A: Y.197, H.199 Ligand excluded by PLIP GOL.6: 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 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: R.18, Y.19, D.20, F.316, S.317, T.318 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: Q.252, I.253, L.303, P.305 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: D.300, K.302, K.304, W.306 Ligands: GOL.12 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: R.301, K.302 Ligands: GOL.15 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain A: K.219, H.220, S.221, S.222 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain A: L.153, Y.154, W.306 Ligands: GOL.9, GOL.16 Ligand excluded by PLIP GOL.13: 1 residues within 4Å: Chain A: Y.47 Ligand excluded by PLIP GOL.14: 2 residues within 4Å: Chain A: R.301 Ligands: GOL.15 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain A: P.158, F.159, I.160, R.301 Ligands: GOL.10, GOL.14, GOL.18 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain A: H.94, F.96, P.97, R.98, K.304, W.306 Ligands: GOL.12 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain A: Q.252, R.255, G.256, D.259, K.405 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain A: I.160, I.161, D.162, G.163, Y.242 Ligands: GOL.15 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain A: A.228, K.235, L.322, E.325 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain A: R.24, Q.28, D.328 Ligand excluded by PLIP

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

ADP.2: 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.3, MG.21, MG.22 19 PLIP interactions: 19 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, 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.3: 23 residues within 4Å: Chain A: Y.19, 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.2, GOL.4, MG.21, MG.22 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.215 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:N.311, A:S.313, A:S.313, A:S.315 Water bridges: A:R.191 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.21: 6 residues within 4Å: Chain A: D.296, E.309, N.311 Ligands: ADP.2, S3A.3, MG.22 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.296, A:E.309, H2O.1 MG.22: 5 residues within 4Å: Chain A: E.309, N.311 Ligands: ADP.2, S3A.3, MG.21 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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