SMTL ID : 7gvm.1

Crystal Structure of B-cell lymphoma 6 protein BTB domain in complex with ligand 4 at 1.40 MGy X-ray dose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x ACE- TRP- VAL- ILE- PRO- ALA: WVIP tetrapeptide(Non-covalent)

ACE-TRP-VAL-ILE-PRO-ALA.1: 12 residues within 4Å: Chain A: C.7, I.8, Q.9, F.10, T.11 Chain B: F.88, R.93, L.94, H.115, V.116, T.119 Ligands: DMS.4 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:F.88, B:L.94, B:L.94, B:V.116, B:T.119, A:I.8, A:I.8, A:F.10, A:F.10, A:F.10 Water bridges: B:T.119, A:R.12 Hydrogen bonds: A:Q.9, A:Q.9, A:T.11, A:T.11 ACE-TRP-VAL-ILE-PRO-ALA.5: 12 residues within 4Å: Chain A: F.88, R.93, L.94, H.115, V.116, T.119 Chain B: C.7, I.8, Q.9, F.10, T.11 Ligands: DMS.8 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.8, B:I.8, B:F.10, B:F.10, B:F.10, A:F.88, A:L.94, A:L.94, A:V.116, A:T.119 Hydrogen bonds: B:Q.9, B:Q.9, B:T.11, A:T.119 Water bridges: B:T.11, B:R.12

2 x 01: 5-[(2,5-dichloropyridin-4-yl)amino]-1,3-dihydro-2H-indol-2-one

01.2: 12 residues within 4Å: Chain A: N.20, R.23, L.24 Chain B: M.50, A.51, C.52, S.53, G.54, Y.57, Q.112, M.113, E.114 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.57 Hydrogen bonds: B:M.50, B:G.54, B:E.114, B:E.114 Water bridges: B:E.114, B:H.115, A:R.27 pi-Stacking: B:Y.57 01.6: 12 residues within 4Å: Chain A: M.50, A.51, C.52, S.53, G.54, Y.57, Q.112, M.113, E.114 Chain B: N.20, R.23, L.24 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.57 Hydrogen bonds: A:M.50, A:G.54, A:E.114 Water bridges: A:Y.57, A:E.114, A:H.115 pi-Stacking: A:Y.57

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: F.88, M.113, H.115, V.116 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: F.88, M.113, H.115, V.116 Ligand excluded by PLIP

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 4 residues within 4Å: Chain A: I.8 Ligands: ACE-TRP-VAL-ILE-PRO-ALA.1, ACE-TRP-VAL-ILE-PRO-ALA.1, ACE-TRP-VAL-ILE-PRO-ALA.1 No protein-ligand interaction detected (PLIP) DMS.8: 4 residues within 4Å: Chain B: I.8 Ligands: ACE-TRP-VAL-ILE-PRO-ALA.5, ACE-TRP-VAL-ILE-PRO-ALA.5, ACE-TRP-VAL-ILE-PRO-ALA.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rodrigues, M.J. et al., Specific radiation damage to halogenated inhibitors and ligands in protein-ligand crystal structures. J.Appl.Crystallogr. (2024)

Release Date

2024-12-11

Peptides

B-cell lymphoma 6 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

B-cell lymphoma 6 protein

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