SMTL ID : 3uec.1

Crystal structure of human Survivin bound to histone H3 phosphorylated on threonine-3.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

2 x ALA- ARG- TPO- LYS: N-TERMINAL FRAGMENT OF HISTONE H3(Non-covalent)

ALA-ARG-TPO-LYS.1: 11 residues within 4Å: Chain A: E.55, L.58, K.66, E.67, L.68, E.69, G.70, W.71, D.75, E.80, H.84 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.58, A:L.58, A:W.71 Hydrogen bonds: A:E.67, A:E.67, A:E.69, A:E.69, A:D.75 Water bridges: A:E.67, A:H.84, A:K.126 Salt bridges: A:K.66, A:E.69, A:H.84 ALA-ARG-TPO-LYS.9: 11 residues within 4Å: Chain B: E.55, L.58, K.66, E.67, L.68, E.69, G.70, W.71, D.75, E.80, H.84 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.58, B:L.58, B:W.71 Hydrogen bonds: B:E.67, B:E.67, B:E.69, B:E.69, B:E.80, B:E.80 Water bridges: B:H.84, B:H.84, B:K.126 Salt bridges: B:K.66, B:E.69, B:H.84

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.61, C.64, H.81, C.88 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.61, A:C.64, A:H.81, A:C.88 ZN.10: 4 residues within 4Å: Chain B: C.61, C.64, H.81, C.88 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.61, B:C.64, B:H.81, B:C.88

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: A.132, V.135, R.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.136 EDO.6: 2 residues within 4Å: Chain A: K.107, E.111 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.107 EDO.11: 3 residues within 4Å: Chain B: A.132, V.135, R.136 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.136 EDO.14: 2 residues within 4Å: Chain B: K.107, E.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.107

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 6 residues within 4Å: Chain A: T.101, G.103, E.104, K.107 Chain B: E.98, E.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.104 PG4.12: 6 residues within 4Å: Chain A: E.98, E.99 Chain B: T.101, G.103, E.104, K.107 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.101, B:E.104 Water bridges: B:E.104

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

1PE.5: 8 residues within 4Å: Chain A: F.17, K.19, R.22, E.44, F.90, L.91, V.93, Q.96 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.17, A:K.19, A:R.22, A:R.22, A:L.91, A:Q.96 Water bridges: A:F.97 1PE.13: 8 residues within 4Å: Chain B: F.17, K.19, R.22, E.44, F.90, L.91, V.93, Q.96 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.17, B:K.19, B:R.22, B:R.22, B:L.91, B:Q.96 Water bridges: B:F.97

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 3 residues within 4Å: Chain A: L.18, K.19, D.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.19, A:D.20, A:D.20 ACT.15: 3 residues within 4Å: Chain B: L.18, K.19, D.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.19, B:D.20

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

PEG.8: 2 residues within 4Å: Chain A: G.34, D.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.74 PEG.16: 2 residues within 4Å: Chain B: G.34, D.74 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niedzialkowska, E. et al., Molecular basis for phosphospecific recognition of histone H3 tails by Survivin paralogues at inner centromeres. Mol.Biol.Cell (2012)

Release Date

2012-03-07

Peptides

Baculoviral IAP repeat-containing protein 5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Baculoviral IAP repeat-containing protein 5

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