SMTL ID : 8xmk.1

Local refinement of SRCR5-9 domains

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: I.725, N.726 No protein-ligand interaction detected (PLIP) NAG.2: 5 residues within 4Å: Chain A: P.894, S.898, L.935, F.943, N.986 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.894, A:F.943 Hydrogen bonds: A:N.986 NAG.9: 3 residues within 4Å: Chain B: N.726, H.732, I.776 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.776 NAG.10: 6 residues within 4Å: Chain B: P.894, S.898, L.935, F.938, F.943, N.986 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.938 Hydrogen bonds: B:S.898, B:N.986 NAG.16: 3 residues within 4Å: Chain C: N.726, H.732, I.776 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.776 NAG.17: 4 residues within 4Å: Chain C: L.935, F.938, F.943, N.986 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.938, C:F.943 Hydrogen bonds: C:N.986

17 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: D.914, D.915, E.981 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.914, A:D.915, A:E.981 CA.4: 4 residues within 4Å: Chain A: H.570, D.572, D.575, F.609 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.570, A:D.572, A:D.575, A:F.609 CA.5: 4 residues within 4Å: Chain A: S.916, D.918, D.921, V.955 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:S.916, A:D.918, A:D.921, A:V.955 CA.6: 3 residues within 4Å: Chain A: D.704, D.705, E.771 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.704, A:D.705, A:E.771 CA.7: 4 residues within 4Å: Chain A: S.706, D.711, M.745, K.746 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.706, A:D.711, A:M.745 CA.8: 7 residues within 4Å: Chain A: C.703, D.705, D.743, E.744, N.766, C.767 Chain B: K.936 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.705, A:D.743, A:D.743, A:E.744 CA.11: 4 residues within 4Å: Chain B: H.570, D.572, D.575, F.609 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.570, B:D.575, B:F.609 CA.12: 3 residues within 4Å: Chain B: D.704, D.705, E.771 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.704, B:D.705, B:E.771 CA.13: 4 residues within 4Å: Chain B: D.705, D.743, E.744, N.766 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.705, B:D.743, B:E.744 CA.14: 5 residues within 4Å: Chain B: S.706, D.708, D.711, M.745, K.746 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.706, B:D.708, B:D.711, B:D.711, B:M.745 CA.15: 4 residues within 4Å: Chain B: S.916, D.918, D.921, V.955 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.916, B:D.918, B:D.921, B:V.955 CA.18: 4 residues within 4Å: Chain C: H.570, D.572, D.575, F.609 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.570, C:D.575, C:F.609 CA.19: 3 residues within 4Å: Chain C: D.704, D.705, E.771 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.704, C:D.705, C:E.771 CA.20: 4 residues within 4Å: Chain C: D.705, D.743, E.744, N.766 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.705, C:D.743, C:E.744 CA.21: 4 residues within 4Å: Chain C: S.706, D.708, D.711, M.745 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:S.706, C:D.708, C:D.711, C:M.745 CA.22: 6 residues within 4Å: Chain C: S.916, D.918, D.921, V.955, K.956, C.957 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:S.916, C:D.918, C:D.921, C:D.921, C:V.955 CA.23: 4 residues within 4Å: Chain B: K.770 Chain C: D.914, D.915, E.981 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.914, C:D.915, C:E.981

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, H. et al., Local refinement of SRCR5-9 domains. To Be Published

Release Date

2025-01-01

Peptides

Scavenger receptor cysteine-rich type 1 protein M130: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Scavenger receptor cysteine-rich type 1 protein M130

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