SMTL ID : 8trs.1

Structure of the EphA2 CRD bound to FabS1CE_C1, trigonal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

19 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 7 residues within 4Å: Chain A: Y.31, S.32, S.33, S.52, Y.55 Chain C: L.93, E.94 Ligand excluded by PLIP EDO.2: 6 residues within 4Å: Chain A: Y.99, A.101, D.103 Chain B: Y.49, Y.55 Chain C: F.82 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: G.9, G.10, T.109, L.110 Ligands: EDO.5 Ligand excluded by PLIP EDO.4: 9 residues within 4Å: Chain A: I.29, Y.30, S.32, M.34, I.51, S.52, S.53, A.72, T.74 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: E.6, S.7, Q.107, G.108, T.109 Ligands: EDO.3 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: A.88, T.91, T.112, V.113, F.147 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: F.27, T.28, R.98, Y.99 Chain C: P.91 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: T.152, V.153, S.154, N.198, N.200 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: Y.54 Chain C: S.124 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: Q.37, K.45, P.59, R.61, F.62, E.81, D.82 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: Q.37, Q.38, K.39, K.42, A.43, K.45 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain A: V.170, L.179, S.180 Chain B: Q.163, S.165, S.179, S.180, T.181 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: K.148, S.150, Y.152, E.198, T.200 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: A.147, K.148, V.149, E.164 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: N.155, E.198, T.207 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain B: R.24, S.67, T.69, D.70 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: P.122, Y.189, N.211, R.212, E.214 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: S.30, S.31 Chain C: L.100, P.101 Ligand excluded by PLIP EDO.41: 7 residues within 4Å: Chain C: R.46, M.47, H.48, L.56, V.57, P.58, I.59 Ligand excluded by PLIP

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 5 residues within 4Å: Chain A: R.19, T.69, Q.82, N.84 Ligands: PEG.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.19, A:T.69, A:N.84 PEG.9: 8 residues within 4Å: Chain A: R.19, S.71, A.72, D.73, K.76, Y.80 Ligands: PEG.8, CL.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.19, A:S.71, A:D.73, A:K.76 PEG.22: 5 residues within 4Å: Chain B: D.1, I.2, Q.27, Y.97, P.98 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.1, B:D.1 Water bridges: B:I.2 PEG.23: 6 residues within 4Å: Chain A: G.42, K.43 Chain B: S.9, Y.87, Q.103, G.104 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.9, B:Y.87 Water bridges: B:K.106, A:Q.39 PEG.24: 5 residues within 4Å: Chain B: P.144, E.146, T.200, Q.201, G.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.202 PEG.26: 2 residues within 4Å: Chain B: P.80, I.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.80 PEG.30: 5 residues within 4Å: Chain B: I.109, K.110, R.111, D.173, S.174 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.110

17 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 2 residues within 4Å: Chain A: S.121, V.122 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: G.66, F.68 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: K.43, G.44 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: G.191, Q.193, T.194, K.211 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: D.209 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: R.87, A.88, E.89 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain A: R.19 Ligands: PEG.9 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain B: Q.27, Y.97 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain B: S.31, S.52 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain B: R.145, A.147, E.164 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain B: P.40, G.41 Ligand excluded by PLIP CL.37: 5 residues within 4Å: Chain B: M.4, T.5, Q.6, G.102, Q.103 Ligand excluded by PLIP CL.38: 3 residues within 4Å: Chain B: P.144, R.145, Y.176 Ligand excluded by PLIP CL.39: 1 residues within 4Å: Chain B: K.39 Ligand excluded by PLIP CL.40: 1 residues within 4Å: Chain B: D.173 Ligand excluded by PLIP CL.42: 3 residues within 4Å: Chain C: K.84, F.85, E.86 Ligand excluded by PLIP CL.43: 3 residues within 4Å: Chain C: E.5, P.14, E.15 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.44: 1 residues within 4Å: Chain C: E.69 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bruce, H.A. et al., Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes. Protein Sci. (2024)

Release Date

2023-11-22

Peptides

S1CE variant of Fab C1 heavy chain: A
S1CE variant of Fab C1 light chain: B
Ephrin type-A receptor 2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

C
D

S1CE variant of Fab C1 heavy chain

S1CE variant of Fab C1 light chain

Ephrin type-A receptor 2

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