SMTL ID : 6vzv.1 (3 other biounits)

TTLL6 bound to gamma-elongation analog

Coordinates

PDB Format

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 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:N.311 Hydrogen bonds: A:Q.130, A:R.169, A:R.169, 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:G.128, 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 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:L.308 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: 7 residues within 4Å: Chain A: K.75, C.129, E.309, N.311 Ligands: S3A.1, ADP.2, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.309, A:E.309, H2O.1 MG.4: 7 residues within 4Å: Chain A: R.191, N.214, D.296, E.309 Ligands: S3A.1, ADP.2, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.296, A:E.309, H2O.1

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: G.131, R.132, G.133, I.134, I.208, L.212 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.131, A:G.133, A:I.134, A:I.134 GOL.6: 6 residues within 4Å: Chain A: S.83, R.98, T.99, W.100, D.105, D.108 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.83, A:S.83, A:R.98, A:R.98, A:D.108, A:D.108 GOL.7: 5 residues within 4Å: Chain A: N.240, E.251, W.254, R.255, R.395 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.240, A:R.255, A:R.255, A:R.395 Water bridges: A:N.186, A:W.254, A:R.395 GOL.8: 5 residues within 4Å: Chain A: R.18, Y.19, D.20, S.317, T.318 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.18, A:D.20, A:T.318, A:T.318, A:T.318 Water bridges: A:S.21, A:R.24, A:R.24 GOL.9: 2 residues within 4Å: Chain A: Q.28, Y.332 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.28 GOL.10: 4 residues within 4Å: Chain A: P.158, F.159, I.160, R.301 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.11: 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.193, A:N.223, A:R.234 GOL.12: 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:K.263, A:K.263, A:K.405 GOL.13: 4 residues within 4Å: Chain A: D.249, E.251, Q.252, R.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.249, A:R.255 GOL.14: 3 residues within 4Å: Chain A: R.24, Q.28, D.328 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.28, A:D.328 Water bridges: A:Q.28 GOL.15: 4 residues within 4Å: Chain A: P.125, G.133, D.148, M.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.133 Water bridges: A:D.148

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

S37.16: 12 residues within 4Å: Chain A: P.97, R.98, Y.112, K.119, L.153, Y.154, I.155, S.156, K.157, D.300, K.302, W.306 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.153, A:K.302 Hydrogen bonds: A:R.98, A:S.156, A:K.157, A:D.300 Water bridges: A:H.94, A:Y.154 Salt 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
TTLL6 unregistered chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
J

Tubulin polyglutamylase TTLL6

TTLL6 unregistered chain

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