SMTL ID : 6tmm.1

BIL2 domain from T.thermophila BUBL1 locus (C1A-N143A)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-mer

Ligands

11 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 3 residues within 4Å: Chain A: S.12, V.129, F.130 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:F.130 Water bridges: A:S.12 FMT.2: 4 residues within 4Å: Chain A: A.19, R.36, Q.46, Q.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.19, A:R.36 FMT.3: 3 residues within 4Å: Chain A: K.103, Y.104, D.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.105 FMT.5: 4 residues within 4Å: Chain A: Q.135, Q.153 Chain D: H.56, E.57 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:K.55, D:H.56, D:E.57, A:Q.135 FMT.8: 3 residues within 4Å: Chain B: D.59, T.124, T.125 No protein-ligand interaction detected (PLIP) FMT.9: 2 residues within 4Å: Chain B: I.2, S.155 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.155 FMT.10: 9 residues within 4Å: Chain B: G.7, G.8, F.10, Y.132, H.133, I.134, F.142, H.150, A.151 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.7, B:I.134 Water bridges: B:H.150 FMT.12: 9 residues within 4Å: Chain C: G.7, G.8, A.9, F.10, Y.132, H.133, I.134, F.142, A.151 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.7, C:I.134 FMT.13: 1 residues within 4Å: Chain C: E.113 No protein-ligand interaction detected (PLIP) FMT.15: 3 residues within 4Å: Chain D: R.6, H.150, M.152 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.6, D:H.150 FMT.16: 9 residues within 4Å: Chain A: L.1 Chain D: N.4, L.5, R.6, G.7, G.8, N.76, R.78, H.93 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.7, D:G.8, D:N.76, D:R.78, A:L.1

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 7 residues within 4Å: Chain A: Q.60, T.74, V.75, N.76 Chain B: P.92, H.93, P.94 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.60, A:V.75, A:N.76

4 x HG: MERCURY (II) ION(Non-covalent)

HG.6: 4 residues within 4Å: Chain A: C.62, V.90, I.120, K.121 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.62, H2O.2, H2O.2 HG.11: 4 residues within 4Å: Chain B: C.62, V.90, I.120, T.122 No protein-ligand interaction detected (PLIP) HG.14: 5 residues within 4Å: Chain C: C.62, V.90, I.120, K.121, T.122 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.62, C:K.121 HG.17: 4 residues within 4Å: Chain D: C.62, V.90, K.121, T.122 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 2 residues within 4Å: Chain A: N.13, H.70 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.70, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chiarini, V. et al., Structural basis of ubiquitination mediated by protein splicing in early Eukarya. Biochim Biophys Acta Gen Subj (2021)

Release Date

2020-12-16

Peptides

NAD(P)(+)--arginine ADP-ribosyltransferase: AC
NAD(P)(+)--arginine ADP-ribosyltransferase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

C
CCC

B
BBB

D
DDD

NAD(P)(+)--arginine ADP-ribosyltransferase

NAD(P)(+)--arginine ADP-ribosyltransferase