SMTL ID : 5l0q.1

Crystal structure of the complex between ADAM10 D+C domain and a conformation specific mAb 8C7.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

hetero-2-2-2-mer

Ligands

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 3 residues within 4Å: Chain A: N.102, I.114, N.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.102 NAG.8: 2 residues within 4Å: Chain C: N.73, S.76 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.73, C:N.73 NAG.12: 3 residues within 4Å: Chain D: N.102, I.114, N.115 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.102, D:N.115 NAG.18: 2 residues within 4Å: Chain F: N.73, S.76 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.73, F:S.76

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

SO4.2: 1 residues within 4Å: Chain A: R.187 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.135, A:R.187, A:R.187 Salt bridges: A:R.187 SO4.3: 3 residues within 4Å: Chain A: S.163, V.164, Q.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.164, A:Q.165 SO4.4: 6 residues within 4Å: Chain A: D.140, C.196, R.197, G.198 Chain C: Y.52, R.54 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:D.140, A:G.198, C:Y.52 Water bridges: A:C.196, C:R.54 Salt bridges: A:R.197, C:R.54 SO4.6: 4 residues within 4Å: Chain A: Q.178 Chain B: Q.27, N.92, R.93 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.27, B:N.92, A:Q.178 Salt bridges: B:R.93 SO4.7: 5 residues within 4Å: Chain B: R.39, R.45, P.59, R.61, E.81 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.45, B:R.61 Salt bridges: B:R.39, B:R.45, B:R.61 SO4.9: 2 residues within 4Å: Chain C: S.25, G.26 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.26 SO4.10: 2 residues within 4Å: Chain C: S.16, S.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.17, C:S.17 SO4.11: 4 residues within 4Å: Chain C: Y.27, T.28, N.31, Y.32 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.28, C:N.31 SO4.13: 2 residues within 4Å: Chain D: R.108, H.109 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.108, D:H.109 SO4.14: 4 residues within 4Å: Chain D: C.196, R.197, G.198 Chain F: Y.52 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain D Hydrogen bonds: F:Y.52, D:G.198 Water bridges: D:R.197, D:R.197 Salt bridges: D:R.197 SO4.16: 5 residues within 4Å: Chain D: Q.178 Chain E: Q.27, N.28, N.92, R.93 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:Q.27, E:N.92, D:Q.178 Salt bridges: E:R.93 SO4.17: 5 residues within 4Å: Chain E: R.39, R.45, P.59, R.61, E.81 7 PLIP interactions: 7 interactions with chain E Water bridges: E:Q.37, E:R.39, E:R.39, E:R.61 Salt bridges: E:R.39, E:R.45, E:R.61 SO4.19: 3 residues within 4Å: Chain F: G.15, S.16, S.17 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.15, F:S.17

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 7 residues within 4Å: Chain A: I.10, C.11, N.13, M.15, E.17, E.20, D.23 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:I.10, A:M.15, A:E.17, A:E.20, A:D.23 MG.15: 6 residues within 4Å: Chain D: I.10, N.13, M.15, E.17, E.20, D.23 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:I.10, D:M.15, D:E.17, D:E.20, D:D.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Atapattu, L. et al., An activated form of ADAM10 is tumor selective and regulates cancer stem-like cells and tumor growth. J.Exp.Med. (2016)

Release Date

2016-11-09

Peptides

Disintegrin and metalloproteinase domain-containing protein 10: AD
mAb 8C7 light chain: BE
mAb 8C7 heavy chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Disintegrin and metalloproteinase domain-containing protein 10

mAb 8C7 light chain

mAb 8C7 heavy chain