SMTL ID : 6j4o.1

Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: L.66, Q.67, Q.70, S.161, L.162, D.172, K.173, P.174 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.173 Water bridges: A:Q.67, A:Q.67, A:L.175 GOL.2: 9 residues within 4Å: Chain A: N.7, K.8, S.9, G.10, F.85, F.86, E.87, T.100, E.103 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.10, A:F.85, A:E.87, A:T.100 Water bridges: A:E.103, A:E.103 GOL.3: 9 residues within 4Å: Chain A: K.74, Y.78, H.80, M.164, S.165, R.166, R.167, A.168, M.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.80 Water bridges: A:Y.78 GOL.4: 6 residues within 4Å: Chain A: W.18, W.22, R.40, N.41 Chain B: R.34, E.38 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.40, B:R.34 Water bridges: A:W.18 GOL.5: 4 residues within 4Å: Chain A: R.167, L.170, Y.191, H.196 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.167, A:H.196 Water bridges: A:S.165, A:S.165, A:R.166, A:Y.191

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 2 residues within 4Å: Chain A: R.57, S.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.59 Salt bridges: A:R.57 PO4.7: 3 residues within 4Å: Chain A: P.54, N.55, Y.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.55, A:Y.122 PO4.8: 4 residues within 4Å: Chain A: K.138, H.147, K.200, K.202 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.202, A:K.202 Salt bridges: A:K.138, A:H.147, A:K.200, A:K.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, N. et al., Structural basis of tubulin detyrosination by the vasohibin-SVBP enzyme complex. Nat.Struct.Mol.Biol. (2019)

Release Date

2019-05-01

Peptides

Tubulinyl-Tyr carboxypeptidase 2: A
Small vasohibin-binding protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tubulinyl-Tyr carboxypeptidase 2

Small vasohibin-binding protein

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