SMTL ID : 3mp8.1

Crystal structure of Sgf29 tudor domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 15 residues within 4Å: Chain A: N.13, D.15, K.16, W.63, A.64, D.66, R.67, E.112, E.154, P.155, Y.156, F.157, W.231, W.341 Ligands: NA.19 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.63, A:R.67, A:R.67, A:Y.156 Water bridges: A:D.66

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: H.65, A.97, Y.177, I.330, M.331, P.332, N.333 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.333, A:N.333 Water bridges: A:Y.177 GOL.3: 1 residues within 4Å: Chain A: K.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.35 Water bridges: A:K.35 GOL.4: 3 residues within 4Å: Chain A: G.433, N.434, S.435 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.434, A:S.435 GOL.5: 2 residues within 4Å: Chain A: Q.366, T.367 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.366 Water bridges: A:T.367, A:T.367 GOL.6: 2 residues within 4Å: Chain A: Y.18, N.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.18, A:N.19 GOL.7: 5 residues within 4Å: Chain A: K.27, N.283, Y.284, E.289 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.27, A:E.289 Water bridges: A:Y.284, A:T.287 GOL.8: 2 residues within 4Å: Chain A: N.186, A.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.187 Water bridges: A:D.185 GOL.9: 3 residues within 4Å: Chain A: Y.177, E.329, I.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.177, A:I.330 Water bridges: A:G.328 GOL.10: 7 residues within 4Å: Chain A: E.23, V.24, K.27, E.289, G.290, A.293 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.27 Water bridges: A:T.287

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 2 residues within 4Å: Chain A: R.421, N.442 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.442 Water bridges: A:R.421 Salt bridges: A:R.399, A:R.421 SO4.12: 3 residues within 4Å: Chain A: P.41, D.42, K.47 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.42 Water bridges: A:H.40, A:D.42 Salt bridges: A:K.47 SO4.13: 3 residues within 4Å: Chain A: K.43, R.345, P.384 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.43, A:N.385, A:N.385, A:N.385, A:A.386 Salt bridges: A:K.43, A:R.345 SO4.14: 2 residues within 4Å: Chain A: D.83, K.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.84 Water bridges: A:A.85 SO4.15: 5 residues within 4Å: Chain A: N.151, Q.153, E.154, D.210, Y.211 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.151, A:Y.211 Water bridges: A:E.154, A:E.154, A:D.210, A:D.210, A:S.212 SO4.16: 5 residues within 4Å: Chain A: S.271, P.272, N.273, K.274, E.275 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.274, A:E.275 Water bridges: A:K.274 Salt bridges: A:K.274

5 x NA: SODIUM ION(Non-functional Binders)

NA.17: 2 residues within 4Å: Chain A: W.159, F.259 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.159 NA.18: 2 residues within 4Å: Chain A: T.250, G.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.250, A:G.253 NA.19: 3 residues within 4Å: Chain A: E.45, E.154 Ligands: GLC-GLC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.45, A:E.45 Water bridges: A:R.345 NA.20: 2 residues within 4Å: Chain A: E.279, N.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.283, A:N.283 Water bridges: A:E.279 NA.21: 4 residues within 4Å: Chain A: K.463, A.477, I.478, D.493 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.477, A:A.477

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.22: 2 residues within 4Å: Chain A: K.483, R.484 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.484 Hydrogen bonds: A:R.484 Salt bridges: A:K.483, A:R.484 ACY.23: 7 residues within 4Å: Chain A: F.492, D.493, G.494, E.495, E.496, E.497, V.498 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.495, A:E.497 ACY.24: 2 residues within 4Å: Chain A: D.42, K.43 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.13, A:K.43 Water bridges: A:N.13, A:L.44

1 x 4BZ: 4-(HYDROXYMETHYL)BENZAMIDINE(Non-covalent)

4BZ.25: 2 residues within 4Å: Chain A: K.306, E.310 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.306, A:K.306 Hydrogen bonds: A:K.306, A:E.310 Water bridges: A:K.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bian, C. et al., Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation. Embo J. (2011)

Release Date

2011-05-04

Peptides

Maltose-binding periplasmic protein,LINKER,SAGA-associated factor 29: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Maltose-binding periplasmic protein,LINKER,SAGA-associated factor 29

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