SMTL ID : 3smt.2 (1 other biounit)

Crystal structure of human SET domain-containing protein3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 16 residues within 4Å: Chain A: R.74, E.102, E.103, F.105, P.179, T.252, R.253, D.274, M.275, C.276, N.277, H.278, Y.312, S.324, F.326, F.328 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:F.105, A:N.277, A:N.277, A:H.278, A:H.278, A:S.324 Water bridges: A:E.103, A:D.183, A:T.252, A:T.252, A:T.252, A:S.324 Salt bridges: A:R.74, A:R.253 pi-Stacking: A:F.326, A:F.326 SAM.18: 16 residues within 4Å: Chain B: R.74, E.102, E.103, F.105, P.179, T.252, R.253, D.274, M.275, C.276, N.277, H.278, Y.312, S.324, F.326, F.328 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:F.105, B:N.277, B:N.277, B:H.278, B:H.278, B:S.324 Water bridges: B:D.183, B:T.252, B:T.252, B:S.324 Salt bridges: B:R.74, B:R.253 pi-Stacking: B:F.326, B:F.326

4 x ARS: ARSENIC(Non-covalent)

ARS.2: 2 residues within 4Å: Chain A: C.296, I.308 No protein-ligand interaction detected (PLIP) ARS.3: 3 residues within 4Å: Chain A: W.273, G.286, C.294 No protein-ligand interaction detected (PLIP) ARS.19: 2 residues within 4Å: Chain B: C.296, I.308 No protein-ligand interaction detected (PLIP) ARS.20: 3 residues within 4Å: Chain B: W.273, G.286, C.294 No protein-ligand interaction detected (PLIP)

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

PG4.4: 5 residues within 4Å: Chain A: F.100, R.108, G.305, E.306, Q.307 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.108, A:Q.307 Water bridges: A:E.306, A:E.306, A:Q.307, A:Q.307 PG4.21: 5 residues within 4Å: Chain B: F.100, R.108, G.305, E.306, Q.307 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.108, B:Q.307 Water bridges: B:E.306, B:Q.307, B:Q.307, B:Q.307

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

ACT.5: 5 residues within 4Å: Chain A: V.366, F.367, A.368, S.377, Q.379 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.368, A:A.368, A:S.377, A:Q.379 Water bridges: A:S.377 ACT.6: 5 residues within 4Å: Chain A: L.340, G.341, F.387, F.428, R.432 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.340, A:F.387, A:F.428 Hydrogen bonds: A:G.341 Water bridges: A:R.432, A:R.432 Salt bridges: A:R.432 ACT.22: 5 residues within 4Å: Chain B: V.366, F.367, A.368, S.377, Q.379 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.368, B:A.368, B:S.377, B:Q.379 Water bridges: B:S.377 ACT.23: 5 residues within 4Å: Chain B: L.340, G.341, F.387, F.428, R.432 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.340, B:F.387, B:F.428 Hydrogen bonds: B:G.341 Water bridges: B:R.432, B:R.432 Salt bridges: B:R.432

22 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.7: 1 residues within 4Å: Chain A: M.97 Ligand excluded by PLIP UNX.8: 3 residues within 4Å: Chain A: D.204, E.319, K.337 Ligand excluded by PLIP UNX.9: 1 residues within 4Å: Chain A: N.211 Ligand excluded by PLIP UNX.10: 2 residues within 4Å: Chain A: Q.208, H.323 Ligand excluded by PLIP UNX.11: 3 residues within 4Å: Chain A: N.153, M.251, Q.254 Ligand excluded by PLIP UNX.12: 2 residues within 4Å: Chain A: G.286, V.297 Ligand excluded by PLIP UNX.13: 2 residues within 4Å: Chain A: R.358 Chain B: F.311 Ligand excluded by PLIP UNX.14: 3 residues within 4Å: Chain A: D.405, F.408 Chain B: H.333 Ligand excluded by PLIP UNX.15: 1 residues within 4Å: Chain A: E.391 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain A: P.140, H.228 Ligand excluded by PLIP UNX.17: 1 residues within 4Å: Chain A: W.419 Ligand excluded by PLIP UNX.24: 1 residues within 4Å: Chain B: M.97 Ligand excluded by PLIP UNX.25: 3 residues within 4Å: Chain B: D.204, E.319, K.337 Ligand excluded by PLIP UNX.26: 1 residues within 4Å: Chain B: N.211 Ligand excluded by PLIP UNX.27: 2 residues within 4Å: Chain B: Q.208, H.323 Ligand excluded by PLIP UNX.28: 3 residues within 4Å: Chain B: N.153, M.251, Q.254 Ligand excluded by PLIP UNX.29: 2 residues within 4Å: Chain B: G.286, V.297 Ligand excluded by PLIP UNX.30: 2 residues within 4Å: Chain A: F.311 Chain B: R.358 Ligand excluded by PLIP UNX.31: 3 residues within 4Å: Chain A: H.333 Chain B: D.405, F.408 Ligand excluded by PLIP UNX.32: 1 residues within 4Å: Chain B: E.391 Ligand excluded by PLIP UNX.33: 2 residues within 4Å: Chain B: P.140, H.228 Ligand excluded by PLIP UNX.34: 1 residues within 4Å: Chain B: W.419 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, H. et al., Crystal structure of human SET domain-containing protein3. To be Published

Release Date

2011-07-20

Peptides

Histone-lysine N-methyltransferase setd3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Histone-lysine N-methyltransferase setd3

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