SMTL ID : 6mlc.1 (1 other biounit)

PHD6 domain of MLL3 in complex with histone H4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-12-6-mer

Ligands

42 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.17, C.26, C.29 Chain B: H.7 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:C.17, A:C.26, A:C.29, B:H.7 ZN.2: 4 residues within 4Å: Chain A: C.35, C.38, H.59, C.62 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.35, A:C.38, A:H.59, A:C.62 ZN.3: 4 residues within 4Å: Chain A: C.51, C.54, C.81, C.84 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.51, A:C.54, A:C.81, A:C.84 ZN.4: 4 residues within 4Å: Chain A: C.5, C.8 Chain B: C.5, C.8 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:C.5, A:C.8, B:C.5, B:C.8 ZN.8: 5 residues within 4Å: Chain A: H.7 Chain B: C.17, W.19, C.26, C.29 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:C.17, B:C.26, B:C.29, A:H.7 ZN.9: 4 residues within 4Å: Chain B: C.35, C.38, H.59, C.62 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.35, B:C.38, B:H.59, B:C.62 ZN.10: 4 residues within 4Å: Chain B: C.51, C.54, C.81, C.84 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.51, B:C.54, B:C.81, B:C.84 ZN.14: 4 residues within 4Å: Chain D: C.17, C.26, C.29 Chain E: H.7 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Metal complexes: D:C.17, D:C.26, D:C.29, E:H.7 ZN.15: 4 residues within 4Å: Chain D: C.35, C.38, H.59, C.62 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.35, D:C.38, D:H.59, D:C.62 ZN.16: 4 residues within 4Å: Chain D: C.51, C.54, C.81, C.84 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.51, D:C.54, D:C.81, D:C.84 ZN.17: 4 residues within 4Å: Chain D: C.5, C.8 Chain E: C.5, C.8 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Metal complexes: E:C.5, E:C.8, D:C.5, D:C.8 ZN.21: 5 residues within 4Å: Chain D: H.7 Chain E: C.17, W.19, C.26, C.29 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain E Metal complexes: D:H.7, E:C.17, E:C.26, E:C.29 ZN.22: 4 residues within 4Å: Chain E: C.35, C.38, H.59, C.62 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.35, E:C.38, E:H.59, E:C.62 ZN.23: 4 residues within 4Å: Chain E: C.51, C.54, C.81, C.84 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.51, E:C.54, E:C.81, E:C.84 ZN.27: 4 residues within 4Å: Chain G: C.17, C.26, C.29 Chain H: H.7 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H Metal complexes: G:C.17, G:C.26, G:C.29, H:H.7 ZN.28: 4 residues within 4Å: Chain G: C.35, C.38, H.59, C.62 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.35, G:C.38, G:H.59, G:C.62 ZN.29: 4 residues within 4Å: Chain G: C.51, C.54, C.81, C.84 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.51, G:C.54, G:C.81, G:C.84 ZN.30: 4 residues within 4Å: Chain G: C.5, C.8 Chain H: C.5, C.8 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain G Metal complexes: H:C.5, H:C.8, G:C.5, G:C.8 ZN.34: 5 residues within 4Å: Chain G: H.7 Chain H: C.17, W.19, C.26, C.29 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain G Metal complexes: H:C.17, H:C.26, H:C.29, G:H.7 ZN.35: 4 residues within 4Å: Chain H: C.35, C.38, H.59, C.62 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.35, H:C.38, H:H.59, H:C.62 ZN.36: 4 residues within 4Å: Chain H: C.51, C.54, C.81, C.84 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.51, H:C.54, H:C.81, H:C.84 ZN.40: 4 residues within 4Å: Chain J: C.17, C.26, C.29 Chain K: H.7 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain K Metal complexes: J:C.17, J:C.26, J:C.29, K:H.7 ZN.41: 4 residues within 4Å: Chain J: C.35, C.38, H.59, C.62 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.35, J:C.38, J:H.59, J:C.62 ZN.42: 4 residues within 4Å: Chain J: C.51, C.54, C.81, C.84 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.51, J:C.54, J:C.81, J:C.84 ZN.43: 4 residues within 4Å: Chain J: C.5, C.8 Chain K: C.5, C.8 4 PLIP interactions: 2 interactions with chain K, 2 interactions with chain J Metal complexes: K:C.5, K:C.8, J:C.5, J:C.8 ZN.47: 5 residues within 4Å: Chain J: H.7 Chain K: C.17, W.19, C.26, C.29 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain J Metal complexes: K:C.17, K:C.26, K:C.29, J:H.7 ZN.48: 4 residues within 4Å: Chain K: C.35, C.38, H.59, C.62 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.35, K:C.38, K:H.59, K:C.62 ZN.49: 4 residues within 4Å: Chain K: C.51, C.54, C.81, C.84 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.51, K:C.54, K:C.81, K:C.84 ZN.53: 4 residues within 4Å: Chain M: C.17, C.26, C.29 Chain N: H.7 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain N Metal complexes: M:C.17, M:C.26, M:C.29, N:H.7 ZN.54: 4 residues within 4Å: Chain M: C.35, C.38, H.59, C.62 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.35, M:C.38, M:H.59, M:C.62 ZN.55: 4 residues within 4Å: Chain M: C.51, C.54, C.81, C.84 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.51, M:C.54, M:C.81, M:C.84 ZN.56: 4 residues within 4Å: Chain M: C.5, C.8 Chain N: C.5, C.8 4 PLIP interactions: 2 interactions with chain N, 2 interactions with chain M Metal complexes: N:C.5, N:C.8, M:C.5, M:C.8 ZN.60: 5 residues within 4Å: Chain M: H.7 Chain N: C.17, W.19, C.26, C.29 4 PLIP interactions: 1 interactions with chain M, 3 interactions with chain N Metal complexes: M:H.7, N:C.17, N:C.26, N:C.29 ZN.61: 4 residues within 4Å: Chain N: C.35, C.38, H.59, C.62 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.35, N:C.38, N:H.59, N:C.62 ZN.62: 4 residues within 4Å: Chain N: C.51, C.54, C.81, C.84 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.51, N:C.54, N:C.81, N:C.84 ZN.66: 4 residues within 4Å: Chain P: C.17, C.26, C.29 Chain Q: H.7 4 PLIP interactions: 3 interactions with chain P, 1 interactions with chain Q Metal complexes: P:C.17, P:C.26, P:C.29, Q:H.7 ZN.67: 4 residues within 4Å: Chain P: C.35, C.38, H.59, C.62 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.35, P:C.38, P:H.59, P:C.62 ZN.68: 4 residues within 4Å: Chain P: C.51, C.54, C.81, C.84 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.51, P:C.54, P:C.81, P:C.84 ZN.69: 4 residues within 4Å: Chain P: C.5, C.8 Chain Q: C.5, C.8 4 PLIP interactions: 2 interactions with chain P, 2 interactions with chain Q Metal complexes: P:C.5, P:C.8, Q:C.5, Q:C.8 ZN.73: 5 residues within 4Å: Chain P: H.7 Chain Q: C.17, W.19, C.26, C.29 4 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain P Metal complexes: Q:C.17, Q:C.26, Q:C.29, P:H.7 ZN.74: 4 residues within 4Å: Chain Q: C.35, C.38, H.59, C.62 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.35, Q:C.38, Q:H.59, Q:C.62 ZN.75: 4 residues within 4Å: Chain Q: C.51, C.54, C.81, C.84 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.51, Q:C.54, Q:C.81, Q:C.84

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: C.5, R.6, G.14, L.15, C.29 Chain B: H.7, C.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.6, A:G.14 Water bridges: A:C.17 GOL.18: 7 residues within 4Å: Chain D: C.5, R.6, G.14, L.15, C.29 Chain E: H.7, C.8 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.6, D:G.14 Water bridges: D:C.17 GOL.31: 7 residues within 4Å: Chain G: C.5, R.6, G.14, L.15, C.29 Chain H: H.7, C.8 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:R.6, G:G.14 Water bridges: G:C.17 GOL.44: 7 residues within 4Å: Chain J: C.5, R.6, G.14, L.15, C.29 Chain K: H.7, C.8 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:R.6, J:G.14 Water bridges: J:C.17 GOL.57: 7 residues within 4Å: Chain M: C.5, R.6, G.14, L.15, C.29 Chain N: H.7, C.8 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:R.6, M:G.14 Water bridges: M:C.17 GOL.70: 7 residues within 4Å: Chain P: C.5, R.6, G.14, L.15, C.29 Chain Q: H.7, C.8 3 PLIP interactions: 3 interactions with chain P Hydrogen bonds: P:R.6, P:G.14 Water bridges: P:C.17

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

UNX.6: 3 residues within 4Å: Chain A: Q.50 Chain B: Q.20 Chain C: G.14 Ligand excluded by PLIP UNX.7: 4 residues within 4Å: Chain A: S.33, S.34, N.41 Chain M: N.73 Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain B: Q.63, R.85 Ligand excluded by PLIP UNX.12: 5 residues within 4Å: Chain A: H.7, C.8 Chain B: L.15, R.16, C.17 Ligand excluded by PLIP UNX.13: 1 residues within 4Å: Chain C: R.17 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain D: Q.50 Chain E: Q.20 Chain F: G.14 Ligand excluded by PLIP UNX.20: 4 residues within 4Å: Chain D: S.33, S.34, N.41 Chain P: N.73 Ligand excluded by PLIP UNX.24: 2 residues within 4Å: Chain E: Q.63, R.85 Ligand excluded by PLIP UNX.25: 5 residues within 4Å: Chain D: H.7, C.8 Chain E: L.15, R.16, C.17 Ligand excluded by PLIP UNX.26: 1 residues within 4Å: Chain F: R.17 Ligand excluded by PLIP UNX.32: 3 residues within 4Å: Chain G: Q.50 Chain H: Q.20 Chain I: G.14 Ligand excluded by PLIP UNX.33: 4 residues within 4Å: Chain G: S.33, S.34, N.41 Chain J: N.73 Ligand excluded by PLIP UNX.37: 2 residues within 4Å: Chain H: Q.63, R.85 Ligand excluded by PLIP UNX.38: 5 residues within 4Å: Chain G: H.7, C.8 Chain H: L.15, R.16, C.17 Ligand excluded by PLIP UNX.39: 1 residues within 4Å: Chain I: R.17 Ligand excluded by PLIP UNX.45: 3 residues within 4Å: Chain J: Q.50 Chain K: Q.20 Chain L: G.14 Ligand excluded by PLIP UNX.46: 4 residues within 4Å: Chain D: N.73 Chain J: S.33, S.34, N.41 Ligand excluded by PLIP UNX.50: 2 residues within 4Å: Chain K: Q.63, R.85 Ligand excluded by PLIP UNX.51: 5 residues within 4Å: Chain J: H.7, C.8 Chain K: L.15, R.16, C.17 Ligand excluded by PLIP UNX.52: 1 residues within 4Å: Chain L: R.17 Ligand excluded by PLIP UNX.58: 3 residues within 4Å: Chain M: Q.50 Chain N: Q.20 Chain O: G.14 Ligand excluded by PLIP UNX.59: 4 residues within 4Å: Chain G: N.73 Chain M: S.33, S.34, N.41 Ligand excluded by PLIP UNX.63: 2 residues within 4Å: Chain N: Q.63, R.85 Ligand excluded by PLIP UNX.64: 5 residues within 4Å: Chain M: H.7, C.8 Chain N: L.15, R.16, C.17 Ligand excluded by PLIP UNX.65: 1 residues within 4Å: Chain O: R.17 Ligand excluded by PLIP UNX.71: 3 residues within 4Å: Chain P: Q.50 Chain Q: Q.20 Chain R: G.14 Ligand excluded by PLIP UNX.72: 4 residues within 4Å: Chain A: N.73 Chain P: S.33, S.34, N.41 Ligand excluded by PLIP UNX.76: 2 residues within 4Å: Chain Q: Q.63, R.85 Ligand excluded by PLIP UNX.77: 5 residues within 4Å: Chain P: H.7, C.8 Chain Q: L.15, R.16, C.17 Ligand excluded by PLIP UNX.78: 1 residues within 4Å: Chain R: R.17 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Structural insights into trans-histone regulation of H3K4 methylation by unique histone H4 binding of MLL3/4. Nat Commun (2019)

Release Date

2018-10-24

Peptides

Histone-lysine N-methyltransferase 2C: ABDEGHJKMNPQ
Histone H4: CFILOR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
A

E
B

G
A

H
B

J
A

K
B

M
A

N
B

P
A

Q
B

C
E

F
E

I
E

L
E

O
E

R
E

Histone-lysine N-methyltransferase 2C

Histone H4

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