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

TTLL6 bound to gamma-elongation analog

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

monomer

Ligands

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

S3A.1: 23 residues within 4Å: Chain A: Y.19, C.129, Q.130, R.169, Y.171, L.189, R.191, N.214, Y.215, S.216, K.233, D.296, E.309, N.311, H.312, S.313, P.314, S.315, D.323, K.327 Ligands: ADP.2, MG.3, MG.4 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:N.311 Hydrogen bonds: A:Q.130, A:R.169, A:R.169, A:Y.171, A:N.214, A:Y.215, A:S.216, A:N.311, A:S.313, A:S.313, A:S.315, A:S.315 Water bridges: A:K.75, A:G.128, A:R.191, A:K.233, A:H.312, A:H.312, A:S.315 Salt bridges: A:R.169, A:R.191, A:R.191, A:K.233, A:H.312, A:K.327

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

ADP.2: 27 residues within 4Å: Chain A: K.75, P.97, I.122, K.124, G.128, 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: S3A.1, MG.3, MG.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.124, 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, A:E.309, A:E.309 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.3: 7 residues within 4Å: Chain A: R.191, N.214, D.296, E.309 Ligands: S3A.1, ADP.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: K.75, C.129, E.309, N.311 Ligands: S3A.1, ADP.2, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.309, A:E.309, H2O.1

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: E.251, R.255, R.395 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.255, A:R.255, A:R.395, A:R.395 GOL.6: 4 residues within 4Å: Chain A: R.18, Y.19, D.20, S.317 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.20, A:D.20, A:S.317 Water bridges: A:S.21 GOL.7: 6 residues within 4Å: Chain A: R.80, R.98, T.99, W.100, D.105, D.108 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.80, A:R.98, A:D.105, A:D.108 Water bridges: A:S.83, A:T.99 GOL.8: 4 residues within 4Å: Chain A: P.158, F.159, I.160, R.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.158, A:I.160 GOL.9: 3 residues within 4Å: Chain A: Q.28, Y.332 Ligands: GOL.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.28 GOL.10: 4 residues within 4Å: Chain A: S.329, Y.332, D.333 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.185, A:G.393 GOL.11: 4 residues within 4Å: Chain A: A.228, F.229, K.235, T.238 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.238 GOL.12: 4 residues within 4Å: Chain A: K.157, P.158, I.160, Y.197 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.157

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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