SMTL ID : 6vzv.4 (3 other biounits)

TTLL6 bound to gamma-elongation analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

hetero-1-1-mer

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 27 PLIP interactions: 27 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:E.309, A:N.311, A:S.313, A:S.313, A:S.315, A:S.315 Water bridges: A:K.75, A:R.191, A:K.233, A:N.311, 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 19 PLIP interactions: 19 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:D.296, A:E.309 Water bridges: A:K.75, 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: 6 residues within 4Å: Chain A: 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.2 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

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: N.240, E.251, W.254, R.255, R.395 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.251, A:R.255, A:R.255, A:R.395, A:R.395 Water bridges: A:N.186, A:N.186, A:N.240, A:R.395 GOL.6: 4 residues within 4Å: Chain A: R.18, Y.19, D.20, S.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.20 Water bridges: A:S.21, A:D.319 GOL.7: 6 residues within 4Å: Chain A: D.92, D.259, K.263, K.405, Y.406, F.409 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.92, A:K.263, A:Y.406 GOL.8: 5 residues within 4Å: Chain A: Y.215, F.224, Q.226, D.319, S.320 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.219, A:D.319 Water bridges: A:S.320, A:S.320 GOL.9: 4 residues within 4Å: Chain A: P.125, G.133, D.148, M.149 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.133 Water bridges: A:D.126, A:D.148 GOL.10: 3 residues within 4Å: Chain A: E.251, Q.252, R.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.255 Water bridges: A:D.249, A:D.249, A:E.251 GOL.11: 5 residues within 4Å: Chain A: S.156, K.157, P.158, I.160, Y.197 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.156, A:P.158

1 x S37: (2~{S})-2-[[[(3~{S})-3-acetamido-4-oxidanyl-4-oxidanylidene-butyl]-oxidanyl-phosphoryl]methyl]pentanedioic acid(Non-covalent)

S37.12: 12 residues within 4Å: Chain A: F.96, P.97, R.98, Y.112, K.119, L.153, Y.154, I.155, S.156, K.157, D.300, W.306 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.98, A:L.153 Hydrogen bonds: A:R.98, A:Y.112, A:S.156, A:K.157 Water bridges: A:H.94, A:S.156 Salt bridges: A:R.98, A:K.119

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
TTLL6 unregistered chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
I

Tubulin polyglutamylase TTLL6

TTLL6 unregistered chain

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