SMTL ID : 5yps.2 (2 other biounits)

The structural basis of histone chaperoneVps75

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.147, E.192, D.193, E.196 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.147, A:E.147, A:E.192, A:D.193, A:E.196 CA.7: 4 residues within 4Å: Chain B: E.147, E.192, D.193, E.196 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.147, B:E.192, B:D.193, B:E.196 CA.8: 3 residues within 4Å: Chain B: D.189, F.191, E.192 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.189, B:D.189, B:F.191

6 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 8 residues within 4Å: Chain A: F.32, D.36 Chain B: Q.43, F.47, Y.51, P.207, N.208, K.211 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.51, B:K.211, B:K.211 1PE.3: 12 residues within 4Å: Chain A: L.40, Q.43, V.44, F.47, N.48, Y.51, V.97, R.99, A.202, E.203, Y.206 Ligands: 1PE.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.43, A:Y.51, A:R.99 1PE.4: 7 residues within 4Å: Chain A: Y.98, P.100, N.101, K.108, Y.125, M.127, L.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.108 Water bridges: A:N.101 1PE.9: 10 residues within 4Å: Chain A: Q.43, F.47, Y.51, P.207, N.208, K.211 Chain B: F.32, D.36, L.39 Ligands: 1PE.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.36 1PE.10: 5 residues within 4Å: Chain B: Y.98, P.100, K.108, Y.125, M.127 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.108 1PE.11: 4 residues within 4Å: Chain B: N.87, H.91, E.117, Y.118 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.87, B:E.117

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: T.179, W.180, S.182, W.183, E.192, E.194 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.179, A:T.179, A:T.179, A:E.194 GOL.13: 5 residues within 4Å: Chain B: E.120, E.159, W.160, K.161 Ligands: GOL.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.120, B:W.160 GOL.14: 3 residues within 4Å: Chain B: E.120, E.159 Ligands: GOL.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.120 GOL.15: 2 residues within 4Å: Chain B: V.44, N.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.48

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 5 residues within 4Å: Chain A: E.70, S.78, I.81, P.83, A.86 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 8 residues within 4Å: Chain B: Q.43, V.44, F.47, N.48, Y.51, V.97, R.99, A.202 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.43, B:R.99, B:A.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Structural basis for the acetylation of histone H3K9 and H3K27 mediated by the histone chaperone Vps75 inPneumocystis carinii. Signal Transduct Target Ther (2019)

Release Date

2018-11-07

Peptides

Vacuolar protein sorting-associated protein 75: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Vacuolar protein sorting-associated protein 75

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