SMTL ID : 6mlc.2 (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 B, 2 interactions with chain A Metal complexes: B:C.5, B:C.8, A:C.5, A: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 D, 2 interactions with chain E Metal complexes: D:C.5, D:C.8, E:C.5, E: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: 3 interactions with chain E, 1 interactions with chain D Metal complexes: E:C.17, E:C.26, E:C.29, D:H.7 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: 1 interactions with chain H, 3 interactions with chain G Metal complexes: H:H.7, G:C.17, G:C.26, G:C.29 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: 1 interactions with chain G, 3 interactions with chain H Metal complexes: G:H.7, H:C.17, H:C.26, H:C.29 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: 1 interactions with chain K, 3 interactions with chain J Metal complexes: K:H.7, J:C.17, J:C.26, J:C.29 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 M, 2 interactions with chain N Metal complexes: M:C.5, M:C.8, N:C.5, N: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: 3 interactions with chain N, 1 interactions with chain M Metal complexes: N:C.17, N:C.26, N:C.29, M:H.7 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

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 11 residues within 4Å: Chain A: Q.50, R.52, V.74, A.75, G.78, F.79 Chain B: Q.20, N.21 Chain C: G.14 Ligands: GOL.6, UNX.13 Ligand excluded by PLIP GOL.6: 9 residues within 4Å: Chain A: R.52, A.75, D.76, I.77 Chain B: Y.23 Chain M: N.21, T.24 Chain N: R.52 Ligands: GOL.5 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain A: W.4, R.6 Chain B: E.18, W.19, Q.20, N.21, N.22 Ligand excluded by PLIP GOL.12: 8 residues within 4Å: Chain A: H.7, C.8 Chain B: C.5, H.7, G.14, L.15, C.29, L.32 Ligand excluded by PLIP GOL.18: 11 residues within 4Å: Chain D: Q.50, R.52, V.74, A.75, G.78, F.79 Chain E: Q.20, N.21 Chain F: G.14 Ligands: GOL.19, UNX.26 Ligand excluded by PLIP GOL.19: 9 residues within 4Å: Chain D: R.52, A.75, D.76, I.77 Chain E: Y.23 Chain P: N.21, T.24 Chain Q: R.52 Ligands: GOL.18 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain D: W.4, R.6 Chain E: E.18, W.19, Q.20, N.21, N.22 Ligand excluded by PLIP GOL.25: 8 residues within 4Å: Chain D: H.7, C.8 Chain E: C.5, H.7, G.14, L.15, C.29, L.32 Ligand excluded by PLIP GOL.31: 11 residues within 4Å: Chain G: Q.50, R.52, V.74, A.75, G.78, F.79 Chain H: Q.20, N.21 Chain I: G.14 Ligands: GOL.32, UNX.39 Ligand excluded by PLIP GOL.32: 9 residues within 4Å: Chain G: R.52, A.75, D.76, I.77 Chain H: Y.23 Chain J: N.21, T.24 Chain K: R.52 Ligands: GOL.31 Ligand excluded by PLIP GOL.37: 7 residues within 4Å: Chain G: W.4, R.6 Chain H: E.18, W.19, Q.20, N.21, N.22 Ligand excluded by PLIP GOL.38: 8 residues within 4Å: Chain G: H.7, C.8 Chain H: C.5, H.7, G.14, L.15, C.29, L.32 Ligand excluded by PLIP GOL.44: 11 residues within 4Å: Chain J: Q.50, R.52, V.74, A.75, G.78, F.79 Chain K: Q.20, N.21 Chain L: G.14 Ligands: GOL.45, UNX.52 Ligand excluded by PLIP GOL.45: 9 residues within 4Å: Chain D: N.21, T.24 Chain E: R.52 Chain J: R.52, A.75, D.76, I.77 Chain K: Y.23 Ligands: GOL.44 Ligand excluded by PLIP GOL.50: 7 residues within 4Å: Chain J: W.4, R.6 Chain K: E.18, W.19, Q.20, N.21, N.22 Ligand excluded by PLIP GOL.51: 8 residues within 4Å: Chain J: H.7, C.8 Chain K: C.5, H.7, G.14, L.15, C.29, L.32 Ligand excluded by PLIP GOL.57: 11 residues within 4Å: Chain M: Q.50, R.52, V.74, A.75, G.78, F.79 Chain N: Q.20, N.21 Chain O: G.14 Ligands: GOL.58, UNX.65 Ligand excluded by PLIP GOL.58: 9 residues within 4Å: Chain G: N.21, T.24 Chain H: R.52 Chain M: R.52, A.75, D.76, I.77 Chain N: Y.23 Ligands: GOL.57 Ligand excluded by PLIP GOL.63: 7 residues within 4Å: Chain M: W.4, R.6 Chain N: E.18, W.19, Q.20, N.21, N.22 Ligand excluded by PLIP GOL.64: 8 residues within 4Å: Chain M: H.7, C.8 Chain N: C.5, H.7, G.14, L.15, C.29, L.32 Ligand excluded by PLIP GOL.70: 11 residues within 4Å: Chain P: Q.50, R.52, V.74, A.75, G.78, F.79 Chain Q: Q.20, N.21 Chain R: G.14 Ligands: GOL.71, UNX.78 Ligand excluded by PLIP GOL.71: 9 residues within 4Å: Chain A: N.21, T.24 Chain B: R.52 Chain P: R.52, A.75, D.76, I.77 Chain Q: Y.23 Ligands: GOL.70 Ligand excluded by PLIP GOL.76: 7 residues within 4Å: Chain P: W.4, R.6 Chain Q: E.18, W.19, Q.20, N.21, N.22 Ligand excluded by PLIP GOL.77: 8 residues within 4Å: Chain P: H.7, C.8 Chain Q: C.5, H.7, G.14, L.15, C.29, L.32 Ligand excluded by PLIP

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

UNX.7: 5 residues within 4Å: Chain A: L.15, R.16, C.17 Chain B: H.7, C.8 No protein-ligand interaction detected (PLIP) UNX.13: 3 residues within 4Å: Chain B: Q.20, N.21 Ligands: GOL.5 No protein-ligand interaction detected (PLIP) UNX.20: 5 residues within 4Å: Chain D: L.15, R.16, C.17 Chain E: H.7, C.8 No protein-ligand interaction detected (PLIP) UNX.26: 3 residues within 4Å: Chain E: Q.20, N.21 Ligands: GOL.18 No protein-ligand interaction detected (PLIP) UNX.33: 5 residues within 4Å: Chain G: L.15, R.16, C.17 Chain H: H.7, C.8 No protein-ligand interaction detected (PLIP) UNX.39: 3 residues within 4Å: Chain H: Q.20, N.21 Ligands: GOL.31 No protein-ligand interaction detected (PLIP) UNX.46: 5 residues within 4Å: Chain J: L.15, R.16, C.17 Chain K: H.7, C.8 No protein-ligand interaction detected (PLIP) UNX.52: 3 residues within 4Å: Chain K: Q.20, N.21 Ligands: GOL.44 No protein-ligand interaction detected (PLIP) UNX.59: 5 residues within 4Å: Chain M: L.15, R.16, C.17 Chain N: H.7, C.8 No protein-ligand interaction detected (PLIP) UNX.65: 3 residues within 4Å: Chain N: Q.20, N.21 Ligands: GOL.57 No protein-ligand interaction detected (PLIP) UNX.72: 5 residues within 4Å: Chain P: L.15, R.16, C.17 Chain Q: H.7, C.8 No protein-ligand interaction detected (PLIP) UNX.78: 3 residues within 4Å: Chain Q: Q.20, N.21 Ligands: GOL.70 No protein-ligand interaction detected (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
C

B
D

D
C

E
D

G
C

H
D

J
C

K
D

M
C

N
D

P
C

Q
D

C
F

F
F

I
F

L
F

O
F

R
F

Histone-lysine N-methyltransferase 2C

Histone H4

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