SMTL ID : 8f47.1

Crystal structure of VACV D13 in complex with STK69439

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-trimer

Ligands

25 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 4 residues within 4Å: Chain A: N.265, Y.544, V.546, K.548 Ligand excluded by PLIP FMT.2: 5 residues within 4Å: Chain A: P.59, Q.60, Y.61 Chain B: L.502, T.503 Ligand excluded by PLIP FMT.3: 5 residues within 4Å: Chain A: P.113, Y.298, Y.308, D.450, I.453 Ligand excluded by PLIP FMT.4: 4 residues within 4Å: Chain A: Y.114, Y.141, I.145, N.497 Ligand excluded by PLIP FMT.5: 4 residues within 4Å: Chain A: P.186, I.254, E.255, K.509 Ligand excluded by PLIP FMT.6: 2 residues within 4Å: Chain A: F.193 Ligands: XDF.24 Ligand excluded by PLIP FMT.7: 1 residues within 4Å: Chain A: L.492 Ligand excluded by PLIP FMT.8: 4 residues within 4Å: Chain A: V.260, I.261, A.269, T.270 Ligand excluded by PLIP FMT.9: 5 residues within 4Å: Chain A: S.97, Y.180, E.236 Chain B: G.482, I.484 Ligand excluded by PLIP FMT.10: 4 residues within 4Å: Chain A: Q.60, Y.61 Chain B: Y.478, S.479 Ligand excluded by PLIP FMT.11: 4 residues within 4Å: Chain B: Y.308, D.450, I.453, F.458 Ligand excluded by PLIP FMT.12: 3 residues within 4Å: Chain B: E.139, S.281, T.499 Ligand excluded by PLIP FMT.13: 5 residues within 4Å: Chain B: P.59, Q.60, Y.61 Chain C: L.502, T.503 Ligand excluded by PLIP FMT.14: 2 residues within 4Å: Chain B: Y.114, N.497 Ligand excluded by PLIP FMT.15: 2 residues within 4Å: Chain B: T.493, F.506 Ligand excluded by PLIP FMT.16: 1 residues within 4Å: Chain B: D.538 Ligand excluded by PLIP FMT.17: 5 residues within 4Å: Chain A: L.502, T.503 Chain C: P.59, Q.60, Y.61 Ligand excluded by PLIP FMT.18: 4 residues within 4Å: Chain C: N.460, K.461, R.486, G.498 Ligand excluded by PLIP FMT.19: 3 residues within 4Å: Chain C: G.289, T.291, N.293 Ligand excluded by PLIP FMT.20: 4 residues within 4Å: Chain C: P.113, Y.298, Y.308, D.450 Ligand excluded by PLIP FMT.21: 4 residues within 4Å: Chain C: K.459, N.460, N.496, N.497 Ligand excluded by PLIP FMT.22: 2 residues within 4Å: Chain C: Y.114, N.497 Ligand excluded by PLIP FMT.23: 2 residues within 4Å: Chain C: F.193 Ligands: XDF.24 Ligand excluded by PLIP FMT.25: 1 residues within 4Å: Chain C: L.492 Ligand excluded by PLIP FMT.26: 1 residues within 4Å: Chain C: R.531 Ligand excluded by PLIP

1 x XDF: 6,8-dimethoxy-2-methylquinolin-4-amine(Non-covalent)

XDF.24: 6 residues within 4Å: Chain A: F.511 Chain B: F.511 Chain C: P.508, F.511 Ligands: FMT.6, FMT.23 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.511, A:F.511

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Subedi, B.P. et al., Structure of scaffolidng protein D13 of Vaccinia Virus in complex with fragments inhibiting A17 binding. To Be Published

Release Date

2023-12-13

Peptides

Scaffold protein D13: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Scaffold protein D13

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