SMTL ID : 6sc5.1

dAb3/HOIP-RBR-Ligand2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-2-mer

Ligands

1 x L6B: methyl 4-[(2-oxidanylidene-5,6,7,8-tetrahydro-1~{H}-quinolin-3-yl)carbonylamino]but-3-enoate(Covalent)

L6B.1: 8 residues within 4Å: Chain A: L.184, C.189, H.191, F.192, H.193, T.195, Q.278, L.285 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.184, A:T.195, A:Q.278, A:L.285 Hydrogen bonds: A:H.191, A:H.193, A:H.193, A:H.193 pi-Stacking: A:F.192

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.3, V.5, C.6, C.26, C.29 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.3, A:C.6, A:C.26, A:C.29 ZN.3: 4 residues within 4Å: Chain A: C.21, C.23, C.48, C.51 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.21, A:C.23, A:C.48, A:C.51 ZN.4: 4 residues within 4Å: Chain A: C.103, C.106, C.121, C.124 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.103, A:C.106, A:C.121, A:C.124 ZN.5: 4 residues within 4Å: Chain A: C.129, C.132, H.140, C.145 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.129, A:C.132, A:H.140, A:C.145 ZN.6: 4 residues within 4Å: Chain A: C.175, C.178, C.194, C.197 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.175, A:C.178, A:C.194, A:C.197 ZN.7: 5 residues within 4Å: Chain A: C.202, C.205, H.230, C.234, F.236 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.202, A:C.205, A:H.230, A:C.234 ZN.8: 4 residues within 4Å: Chain A: C.215, C.220, H.227, H.229 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.215, A:C.220, A:H.227, A:H.229 ZN.9: 4 residues within 4Å: Chain A: C.273, C.290, C.302, H.305 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.273, A:C.290, A:C.302, A:H.305

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 5 residues within 4Å: Chain A: N.207, P.231, L.367, G.368, Q.369 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.207, A:Q.369 Water bridges: A:N.207, A:Q.369, A:Q.369, A:S.370, A:S.370 SO4.11: 6 residues within 4Å: Chain A: G.188, C.189, M.190, H.191, F.236, R.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.190, A:H.191 Salt bridges: A:R.239 SO4.13: 6 residues within 4Å: Chain B: S.52, P.53, I.54, G.55, T.56, Y.57 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.52, B:I.54, B:G.55, B:T.56, B:T.56, B:T.56 SO4.14: 3 residues within 4Å: Chain B: F.27, T.28, Y.32 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:Y.32

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

CL.12: 5 residues within 4Å: Chain A: L.101, W.102, K.133 Chain B: R.103, G.104 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsai, Y.I. et al., Single-Domain Antibodies as Crystallization Chaperones to Enable Structure-Based Inhibitor Development for RBR E3 Ubiquitin Ligases. Cell Chem Biol (2020)

Release Date

2019-11-27

Peptides

E3 ubiquitin-protein ligase RNF31: A
Single domain antibody: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E3 ubiquitin-protein ligase RNF31

Single domain antibody

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