SMTL ID : 6d01.1 (1 other biounit)

Crystal structure of 1210 Fab in complex with circumsporozoite protein NANP5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-2-2-1-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: S.56, K.57, K.58, Y.59 Ligand excluded by PLIP EDO.2: 3 residues within 4Å: Chain A: D.54, R.72, N.74 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: S.25, G.26, N.77 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: Y.60, D.62 Chain B: D.1, Y.94 Ligands: PEG.5 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain B: Q.37, K.45, L.47, P.59, F.62, D.81, D.82 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain B: S.67, G.68, T.69 Ligands: EDO.11 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain B: Q.27, S.28 Chain D: K.50 Ligands: EDO.19 Ligand excluded by PLIP EDO.9: 1 residues within 4Å: Chain B: K.50 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: L.151, V.179, S.187, L.188, S.189 Chain B: S.161, S.175, T.177 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain B: S.28, G.68 Ligands: EDO.7 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain B: K.39, K.42 Ligands: EDO.13 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain B: K.42 Ligands: EDO.12 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: Q.39 Chain B: Q.38, K.39, P.40, G.41, K.42 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: D.1, Q.27, N.93 Ligands: EDO.16 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: N.93 Chain C: D.101, S.103 Ligands: EDO.15 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: Q.27, N.92, N.93 Chain C: S.103, D.104 Ligands: EDO.8, EDO.20 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain C: S.102, D.104, Y.106, D.108 Chain D: W.32, K.50 Ligands: EDO.19 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain C: G.44, L.45 Chain D: G.98, Q.99 Ligands: PEG.22 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain D: G.64, S.65, G.66 Ligands: EDO.28 Ligand excluded by PLIP EDO.24: 1 residues within 4Å: Chain D: R.107 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain C: L.151, V.179, S.187, L.188, S.189 Chain D: Q.159, S.175, T.177 Ligand excluded by PLIP EDO.26: 1 residues within 4Å: Chain D: Q.154 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain D: R.18, S.63 Ligands: PEG.31 Ligand excluded by PLIP EDO.28: 1 residues within 4Å: Ligands: EDO.23 Ligand excluded by PLIP EDO.29: 1 residues within 4Å: Chain D: S.67 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain D: Q.37, K.45, P.59, F.62, D.81, D.82 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain A: W.52 Chain E: N.15, N.17 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain A: Y.105 Chain C: W.52 Chain E: A.6, N.7, N.11 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain A: D.101, S.103 Chain E: N.19 Ligand excluded by PLIP

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

PEG.5: 8 residues within 4Å: Chain A: E.46, W.47, A.61 Chain B: D.1, Y.94, W.95, T.96 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.46, A:E.46 PEG.17: 3 residues within 4Å: Chain B: Q.159, E.160, V.162 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.159, B:V.162 PEG.18: 4 residues within 4Å: Chain B: K.106, R.107, D.169, S.170 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.107, B:R.107, B:S.170, B:S.170 PEG.22: 9 residues within 4Å: Chain C: L.45, E.46, W.47 Chain D: D.1, I.2, W.95, T.96, F.97 Ligands: EDO.21 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.1, D:F.97, C:W.47, C:W.47 PEG.31: 4 residues within 4Å: Chain D: R.18, S.63, S.76 Ligands: EDO.27 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.18, D:R.18, D:L.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imkeller, K. et al., Antihomotypic affinity maturation improves human B cell responses against a repetitive epitope. Science (2018)

Release Date

2018-06-13

Peptides

1210 Antibody, heavy chain: AC
1210 Antibody, Light chain: BD
NANP5: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
I

1210 Antibody, heavy chain

1210 Antibody, Light chain

NANP5

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