SMTL ID : 6cko.1

Crystal structure of an AF10 fragment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-4-4-mer

Ligands

16 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: E.56 Chain B: H.16 Chain H: D.5 Ligands: UNX.6 5 PLIP interactions: 2 interactions with chain H, 2 interactions with chain A, 1 interactions with chain B Metal complexes: H:D.5, H:D.5, A:E.56, A:E.56, B:H.16 ZN.2: 4 residues within 4Å: Chain A: E.19, H.46 Ligands: UNX.4, UNX.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.19, A:E.19, A:H.46 ZN.3: 3 residues within 4Å: Chain A: E.57 Ligands: UNX.9, UNX.10 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.57 ZN.12: 4 residues within 4Å: Chain B: H.29, E.33 Chain D: D.30 Ligands: UNX.13 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Metal complexes: B:H.29, B:E.33, D:D.30, D:D.30 ZN.20: 4 residues within 4Å: Chain C: E.56 Chain D: H.16 Chain F: D.5 Ligands: UNX.25 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 interactions with chain F Metal complexes: C:E.56, C:E.56, D:H.16, F:D.5, F:D.5 ZN.21: 4 residues within 4Å: Chain C: E.19, H.46 Ligands: UNX.23, UNX.24 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.19, C:E.19, C:H.46 ZN.22: 3 residues within 4Å: Chain C: E.57 Ligands: UNX.28, UNX.29 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.57 ZN.31: 4 residues within 4Å: Chain B: D.30 Chain D: H.29, E.33 Ligands: UNX.32 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Metal complexes: D:H.29, D:E.33, B:D.30, B:D.30 ZN.39: 4 residues within 4Å: Chain D: D.5 Chain E: E.56 Chain F: H.16 Ligands: UNX.42 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 1 interactions with chain E Metal complexes: D:D.5, F:H.16, E:E.56 ZN.40: 4 residues within 4Å: Chain E: E.19, H.46 Ligands: UNX.43, UNX.44 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.19, E:E.19, E:H.46 ZN.41: 1 residues within 4Å: Chain E: E.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.15 ZN.46: 3 residues within 4Å: Chain F: H.29 Ligands: UNX.49, UNX.50 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:H.29 ZN.52: 4 residues within 4Å: Chain B: D.5 Chain G: E.56 Chain H: H.16 Ligands: UNX.55 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain G, 1 interactions with chain H Metal complexes: B:D.5, G:E.56, H:H.16 ZN.53: 4 residues within 4Å: Chain G: E.19, H.46 Ligands: UNX.56, UNX.57 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.19, G:E.19, G:H.46 ZN.54: 1 residues within 4Å: Chain G: E.15 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.15 ZN.59: 3 residues within 4Å: Chain H: H.29 Ligands: UNX.62, UNX.63 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:H.29

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

UNX.4: 5 residues within 4Å: Chain A: E.19, W.22, H.46 Ligands: ZN.2, UNX.5 Ligand excluded by PLIP UNX.5: 5 residues within 4Å: Chain A: E.19, H.46, V.50 Ligands: ZN.2, UNX.4 Ligand excluded by PLIP UNX.6: 6 residues within 4Å: Chain A: E.56 Chain B: H.16, L.20 Chain H: G.1, D.5 Ligands: ZN.1 Ligand excluded by PLIP UNX.7: 7 residues within 4Å: Chain A: A.74, S.77 Chain C: A.74, S.77 Ligands: UNX.8, UNX.26, UNX.27 Ligand excluded by PLIP UNX.8: 6 residues within 4Å: Chain A: A.74, S.77 Chain C: S.77 Ligands: UNX.7, UNX.26, UNX.27 Ligand excluded by PLIP UNX.9: 3 residues within 4Å: Chain A: E.57 Ligands: ZN.3, UNX.10 Ligand excluded by PLIP UNX.10: 4 residues within 4Å: Chain A: R.54, E.57 Ligands: ZN.3, UNX.9 Ligand excluded by PLIP UNX.11: 3 residues within 4Å: Chain D: E.33, L.34 Ligands: UNX.30 Ligand excluded by PLIP UNX.13: 6 residues within 4Å: Chain B: H.29, E.33 Chain D: Q.23, L.27, D.30 Ligands: ZN.12 Ligand excluded by PLIP UNX.14: 4 residues within 4Å: Chain A: N.73 Chain B: L.34, Q.37 Ligands: UNX.33 Ligand excluded by PLIP UNX.15: 1 residues within 4Å: Chain B: E.33 Ligand excluded by PLIP UNX.16: 3 residues within 4Å: Chain B: L.40, K.43, A.44 Ligand excluded by PLIP UNX.17: 4 residues within 4Å: Chain A: E.51, R.54 Chain B: R.21 Ligands: UNX.18 Ligand excluded by PLIP UNX.18: 3 residues within 4Å: Chain A: L.55, Q.58 Ligands: UNX.17 Ligand excluded by PLIP UNX.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.23: 5 residues within 4Å: Chain C: E.19, W.22, H.46 Ligands: ZN.21, UNX.24 Ligand excluded by PLIP UNX.24: 5 residues within 4Å: Chain C: E.19, H.46, V.50 Ligands: ZN.21, UNX.23 Ligand excluded by PLIP UNX.25: 6 residues within 4Å: Chain C: E.56 Chain D: H.16, L.20 Chain F: G.1, D.5 Ligands: ZN.20 Ligand excluded by PLIP UNX.26: 7 residues within 4Å: Chain A: A.74, S.77 Chain C: A.74, S.77 Ligands: UNX.7, UNX.8, UNX.27 Ligand excluded by PLIP UNX.27: 6 residues within 4Å: Chain A: S.77 Chain C: A.74, S.77 Ligands: UNX.7, UNX.8, UNX.26 Ligand excluded by PLIP UNX.28: 3 residues within 4Å: Chain C: E.57 Ligands: ZN.22, UNX.29 Ligand excluded by PLIP UNX.29: 4 residues within 4Å: Chain C: R.54, E.57 Ligands: ZN.22, UNX.28 Ligand excluded by PLIP UNX.30: 3 residues within 4Å: Chain B: E.33, L.34 Ligands: UNX.11 Ligand excluded by PLIP UNX.32: 6 residues within 4Å: Chain B: Q.23, L.27, D.30 Chain D: H.29, E.33 Ligands: ZN.31 Ligand excluded by PLIP UNX.33: 4 residues within 4Å: Chain C: N.73 Chain D: L.34, Q.37 Ligands: UNX.14 Ligand excluded by PLIP UNX.34: 1 residues within 4Å: Chain D: E.33 Ligand excluded by PLIP UNX.35: 3 residues within 4Å: Chain D: L.40, K.43, A.44 Ligand excluded by PLIP UNX.36: 4 residues within 4Å: Chain C: E.51, R.54 Chain D: R.21 Ligands: UNX.37 Ligand excluded by PLIP UNX.37: 3 residues within 4Å: Chain C: L.55, Q.58 Ligands: UNX.36 Ligand excluded by PLIP UNX.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.42: 5 residues within 4Å: Chain D: D.5 Chain E: N.52, E.56 Chain F: H.16 Ligands: ZN.39 Ligand excluded by PLIP UNX.43: 6 residues within 4Å: Chain E: E.19, W.22, H.46, Q.47 Ligands: ZN.40, UNX.44 Ligand excluded by PLIP UNX.44: 5 residues within 4Å: Chain E: E.19, H.46, V.50 Ligands: ZN.40, UNX.43 Ligand excluded by PLIP UNX.45: 1 residues within 4Å: Chain E: Q.75 Ligand excluded by PLIP UNX.47: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.48: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.49: 3 residues within 4Å: Chain F: H.29 Ligands: ZN.46, UNX.50 Ligand excluded by PLIP UNX.50: 4 residues within 4Å: Chain F: H.29, E.33 Ligands: ZN.46, UNX.49 Ligand excluded by PLIP UNX.51: 1 residues within 4Å: Chain F: E.33 Ligand excluded by PLIP UNX.55: 5 residues within 4Å: Chain B: D.5 Chain G: N.52, E.56 Chain H: H.16 Ligands: ZN.52 Ligand excluded by PLIP UNX.56: 6 residues within 4Å: Chain G: E.19, W.22, H.46, Q.47 Ligands: ZN.53, UNX.57 Ligand excluded by PLIP UNX.57: 5 residues within 4Å: Chain G: E.19, H.46, V.50 Ligands: ZN.53, UNX.56 Ligand excluded by PLIP UNX.58: 1 residues within 4Å: Chain G: Q.75 Ligand excluded by PLIP UNX.60: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.61: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.62: 3 residues within 4Å: Chain H: H.29 Ligands: ZN.59, UNX.63 Ligand excluded by PLIP UNX.63: 4 residues within 4Å: Chain H: H.29, E.33 Ligands: ZN.59, UNX.62 Ligand excluded by PLIP UNX.64: 1 residues within 4Å: Chain H: E.33 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., Structural and functional analysis of the DOT1L-AF10 complex reveals mechanistic insights into MLL-AF10-associated leukemogenesis. Genes Dev. (2018)

Release Date

2018-03-21

Peptides

Protein AF-10: ACEG
Histone-lysine N-methyltransferase, H3 lysine-79 specific: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
B

G
B

B
C

D
C

F
D

H
D

Protein AF-10

Histone-lysine N-methyltransferase, H3 lysine-79 specific

Related Entries With Identical Sequence