SMTL ID : 8et0.1

Crystal Complex of murine Cyclooxygenase-2 with alpaca nanobody F9

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: E.109, N.113, Y.116, R.185, F.189 Chain B: L.207 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: L.207 Chain B: E.109, N.113, Y.116, R.185, F.189 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.185 Water bridges: A:D.208, A:D.208

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

NAG.3: 3 residues within 4Å: Chain A: Y.23, E.35, N.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.23, A:N.36 NAG.4: 5 residues within 4Å: Chain A: Q.375, N.379, S.381, I.382, E.385 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.379 NAG.6: 5 residues within 4Å: Chain B: S.6, P.8, Y.23, E.35, N.36 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.8 Hydrogen bonds: B:Y.23, B:Y.23 NAG.7: 5 residues within 4Å: Chain B: Q.375, N.379, S.381, I.382, E.385 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.379

2 x IBP: IBUPROFEN(Non-covalent)

IBP.5: 12 residues within 4Å: Chain A: V.85, R.89, V.318, S.322, Y.324, L.328, W.356, M.491, V.492, G.495, A.496, L.500 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.318, A:Y.324, A:L.328, A:W.356, A:A.496 Salt bridges: A:R.89 IBP.8: 13 residues within 4Å: Chain B: V.85, R.89, V.318, S.322, Y.324, L.328, W.356, M.491, V.492, G.495, A.496, S.499, L.500 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.318, B:Y.324, B:L.328, B:W.356, B:A.496 Hydrogen bonds: B:Y.324, B:Y.324 Salt bridges: B:R.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, S. et al., Crystal complex of murine cycloxygenase-2 with alpaca nanobody F9. To Be Published

Release Date

2023-10-18

Peptides

Prostaglandin G/H synthase 2: AB
anti-cox-2 alpaca nanobody F9: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Prostaglandin G/H synthase 2

anti-cox-2 alpaca nanobody F9

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