SMTL ID : 4o61.2 (1 other biounit)

Structure of human ALKBH5 crystallized in the presence of citrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: A.42, G.45, L.46, Y.47, V.52, R.54 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.41, A:A.42, A:Y.47, A:R.54, A:R.54 Water bridges: A:E.49

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 12 residues within 4Å: Chain A: K.60, N.121, I.129, H.132, D.134, I.143, S.145, H.194, I.209, R.211 Ligands: UNX.4, UNX.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.121, A:D.134, A:S.145 Water bridges: A:R.211, A:R.211 Salt bridges: A:K.60, A:H.132, A:H.132, A:H.194, A:H.194, A:R.211, A:R.211

1 x UNL: UNKNOWN LIGAND

UNL.3: 6 residues within 4Å: Chain A: V.39, A.42, E.43, R.54, N.59, Y.61 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.42, A:R.54, A:N.59, A:Y.61, A:Y.61 Water bridges: A:E.43

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

UNX.4: 4 residues within 4Å: Chain A: R.58, K.60 Ligands: CIT.2, UNX.12 No protein-ligand interaction detected (PLIP) UNX.5: 5 residues within 4Å: Chain A: I.129, I.196, R.205, V.207 Ligands: CIT.2 No protein-ligand interaction detected (PLIP) UNX.6: 2 residues within 4Å: Chain A: Q.5, E.9 No protein-ligand interaction detected (PLIP) UNX.7: 4 residues within 4Å: Chain A: A.55, P.56, L.57, R.58 No protein-ligand interaction detected (PLIP) UNX.8: 3 residues within 4Å: Chain A: P.78, G.79, E.81 No protein-ligand interaction detected (PLIP) UNX.9: 3 residues within 4Å: Chain A: E.32, F.149, R.178 No protein-ligand interaction detected (PLIP) UNX.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.11: 5 residues within 4Å: Chain A: F.63, E.65, S.117, A.118, V.119 No protein-ligand interaction detected (PLIP) UNX.12: 5 residues within 4Å: Chain A: R.58, N.121, Y.123, I.129 Ligands: UNX.4 No protein-ligand interaction detected (PLIP) UNX.13: 2 residues within 4Å: Chain A: G.64, N.116 No protein-ligand interaction detected (PLIP) UNX.14: 1 residues within 4Å: Chain A: N.116 No protein-ligand interaction detected (PLIP) UNX.15: 2 residues within 4Å: Chain A: I.92, H.97 No protein-ligand interaction detected (PLIP) UNX.16: 5 residues within 4Å: Chain A: G.64, P.85, G.87, D.88, V.89 No protein-ligand interaction detected (PLIP) UNX.17: 2 residues within 4Å: Chain A: S.150, D.151 No protein-ligand interaction detected (PLIP) UNX.18: 1 residues within 4Å: Chain A: R.178 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, C. et al., Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation. J.Biol.Chem. (2014)

Release Date

2014-02-26

Peptides

RNA demethylase ALKBH5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

RNA demethylase ALKBH5

Related Entries With Identical Sequence