SMTL ID : 8esv.1

Structure of human ADAM10-Tspan15 complex bound to 11G2 vFab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.1: 13 residues within 4Å: Chain A: Q.22, T.23, D.24, R.71, N.73, D.77, D.80, T.82, N.83, P.84, F.85, Q.102, V.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.102

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.2: 7 residues within 4Å: Chain A: H.188, S.190, G.191, T.192, C.230, R.233, N.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.192, A:T.192, A:S.190, A:S.190, A:S.190

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

NAG.3: 5 residues within 4Å: Chain A: P.343, K.344, N.346, I.358, N.359 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.343 Hydrogen bonds: A:I.358, A:N.359

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 7 residues within 4Å: Chain A: I.254, C.255, G.256, N.257, M.259, E.264, D.267 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:M.259, A:E.264, A:D.267

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: H.178, H.182, H.188 Ligands: BAT.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.178, A:H.182, A:H.188

1 x BAT: 4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE(Non-covalent)

BAT.6: 17 residues within 4Å: Chain A: G.121, V.122, L.123, G.124, L.125, A.126, N.162, T.175, H.178, E.179, H.182, H.188, Y.213, A.214, R.215, A.216 Ligands: ZN.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.122, A:L.125, A:H.178 Hydrogen bonds: A:G.121, A:L.123, A:G.124, A:A.126, A:A.214, A:A.216 pi-Stacking: A:H.188

2 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 4 residues within 4Å: Chain B: V.124, F.128, Q.131, T.132 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.128 Y01.8: 7 residues within 4Å: Chain B: L.101, Y.102, Q.105, A.106, Y.109, I.110, I.113 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.102, B:Y.102, B:Q.105, B:A.106, B:Y.109, B:Y.109, B:I.110, B:I.113 Hydrogen bonds: B:Q.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lipper, C.H. et al., Structural basis for membrane-proximal proteolysis of substrates by ADAM10. Cell (2023)

Release Date

2023-06-14

Peptides

Disintegrin and metalloproteinase domain-containing protein 10: A
Tetraspanin-15: B
11G2 Fab Heavy Chain: C
11G2 Fab Light Chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

Membrane

We predict this structure to be a membrane protein.
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Disintegrin and metalloproteinase domain-containing protein 10

Tetraspanin-15

11G2 Fab Heavy Chain

11G2 Fab Light Chain