SMTL ID : 3u88.1 (1 other biounit)

Crystal structure of human menin in complex with MLL1 and LEDGF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x CHD: CHOLIC ACID(Non-covalent)

CHD.1: 4 residues within 4Å: Chain A: S.132, Y.133, F.134, K.135 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.134 Hydrogen bonds: A:S.132, A:K.135 Salt bridges: A:K.135

4 x GGB: L-CANAVANINE(Non-covalent)

GGB.2: 4 residues within 4Å: Chain A: Y.133, F.134, R.137, K.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.134, A:R.137 GGB.4: 8 residues within 4Å: Chain A: R.108, G.111, V.112, S.113, G.169, L.170, R.171, D.172 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.108, A:G.111, A:V.112 Salt bridges: A:R.171, A:D.172 GGB.12: 3 residues within 4Å: Chain C: R.59, K.61 Ligands: GGB.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.59 GGB.13: 4 residues within 4Å: Chain C: L.17, K.18, I.19 Ligands: GGB.12 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.19 Hydrogen bonds: C:K.14, C:I.19

1 x 0BR: (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol(Non-covalent)

0BR.3: 8 residues within 4Å: Chain A: W.126, L.129, S.130, R.131, Y.133, K.135, W.198, N.203 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.126, A:K.135, A:W.198, A:W.198 pi-Cation interactions: A:R.131

4 x GLV: GLYOXYLIC ACID(Non-covalent)

GLV.5: 7 residues within 4Å: Chain A: K.135, D.136, D.153, S.154, W.198, G.200 Chain B: W.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.154, A:S.154, A:S.154, A:G.200 GLV.6: 7 residues within 4Å: Chain A: E.195, T.197, H.199, D.205, R.206, Y.222, E.356 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.199, A:R.206, A:Y.222 Salt bridges: A:H.181 GLV.7: 5 residues within 4Å: Chain A: E.408, A.411, H.412, R.415, L.491 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.412, A:R.415 Salt bridges: A:H.412 GLV.14: 4 residues within 4Å: Chain A: R.98 Chain C: R.58, T.71, N.75 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.75 Salt bridges: C:R.58, A:R.98

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

SO4.8: 2 residues within 4Å: Chain A: K.377, R.446 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.377, A:R.446 SO4.9: 2 residues within 4Å: Chain A: R.275, Y.312 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.275 SO4.10: 7 residues within 4Å: Chain A: R.330 Chain B: G.10, T.11, G.12, R.13, R.14, G.15 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.330, B:T.11, B:G.12, B:R.13, B:R.14, B:G.15 Salt bridges: B:R.14 SO4.11: 6 residues within 4Å: Chain A: G.2 Chain B: L.48, R.52, G.56, E.57 Chain C: K.78 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Salt bridges: B:R.52, C:K.78 Hydrogen bonds: A:G.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, J. et al., The same pocket in menin binds both MLL and JUND but has opposite effects on transcription. Nature (2012)

Release Date

2012-02-15

Peptides

Menin: A
Histone-lysine N-methyltransferase 2A: B
Lens epithelium-derived growth factor: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
M

C
C

Menin

Histone-lysine N-methyltransferase 2A

Lens epithelium-derived growth factor

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