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SMTL ID : 6kix.1

Cryo-EM structure of human MLL1-NCP complex, binding mode1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-1-1-1-1-mer

Ligands

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Covalent)

SAH.1:

11 residues within 4Å:

Chain L: H.86, G.87, R.88, C.129, Y.130, F.151, N.153, H.154, Y.191, C.204, N.205

9 PLIP interactions:

9 interactions with chain L

Hydrogen bonds: L:R.88, L:R.88, L:Y.130, L:Y.130, L:H.154, L:H.154, L:N.205
Salt bridges: L:H.86, L:R.88

1 x ZN: ZINC ION(Non-covalent)

ZN.2:

5 residues within 4Å:

Chain L: C.204, N.205, C.206, G.207, C.211

3 PLIP interactions:

3 interactions with chain L

Metal complexes: L:C.204, L:C.204, L:C.206

1 x LYS: LYSINE(Non-covalent)

LYS.3:

8 residues within 4Å:

Chain L: Y.105, C.129, Y.130, M.131, F.132, R.133, Y.191
Ligands: GLN.4

6 PLIP interactions:

6 interactions with chain L,

Hydrophobic interactions: L:F.132, L:Y.191
Hydrogen bonds: L:Y.105, L:M.131, L:R.133, L:Y.191

1 x GLN: GLUTAMINE(Non-covalent)

GLN.4:

5 residues within 4Å:

Chain L: F.132, R.133, Y.191, K.192
Ligands: LYS.3

4 PLIP interactions:

4 interactions with chain L,

Hydrophobic interactions: L:K.192
Hydrogen bonds: L:R.133, L:Y.191, L:K.192

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Xue, H. et al., Structural basis of nucleosome recognition and modification by MLL methyltransferases. Nature (2019)

Release Date

2019-09-11

Peptides

Histone H3: AE
Histone H4: BF
Histone H2A: CG
Histone H2B 1.1: DH
Retinoblastoma-binding protein 5: K
Histone-lysine N-methyltransferase 2A: L
WD repeat-containing protein 5: M
Set1/Ash2 histone methyltransferase complex subunit ASH2: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

K
N

L
K

M
R

N
T

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Histone H3

Toggle Identical (AE)

Histone H4

Histone H2A

Histone H2B 1.1

Retinoblastoma-binding protein 5

Histone-lysine N-methyltransferase 2A

WD repeat-containing protein 5

Set1/Ash2 histone methyltransferase complex subunit ASH2

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