SMTL ID : 6b5s.1

Structure of PfCSP peptide 25 with human antibody CIS42

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-1-1-1-mer

Ligands

9 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.1: 8 residues within 4Å: Chain A: L.11, L.114, T.116, F.152, P.153, E.154, Y.182 Ligands: NA.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.154, A:Y.182 IPA.2: 7 residues within 4Å: Chain A: I.51, G.56, S.71, F.72 Ligands: NH4.8, NH4.18, NA.26 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.72 IPA.3: 7 residues within 4Å: Chain A: S.9, V.93, Q.111, G.112, T.113, L.114 Chain B: G.43 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.114 IPA.4: 7 residues within 4Å: Chain A: Q.39, A.40, P.41, G.42, A.92, V.93, L.114 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.41 IPA.5: 6 residues within 4Å: Chain A: R.98, Y.100, V.104, D.107, Y.108 Ligands: NA.46 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.100 Hydrogen bonds: A:D.107 IPA.6: 3 residues within 4Å: Chain A: G.26, Y.27, T.28 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.26, A:Y.27 IPA.30: 10 residues within 4Å: Chain A: Q.39, G.42, Q.43, G.44 Chain B: D.87, Y.89, G.103, G.104, T.105, K.106 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.87, B:K.106 Hydrogen bonds: B:G.104 Water bridges: B:K.106, A:G.44 IPA.31: 10 residues within 4Å: Chain B: Q.39, H.41, K.47, S.61, R.63, F.64, E.83, D.84 Ligands: NH4.37, NH4.38 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.64 Hydrogen bonds: B:Q.39, B:D.84 IPA.32: 4 residues within 4Å: Chain B: R.56, S.58, G.59, N.62 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.56

26 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.7: 6 residues within 4Å: Chain A: K.19, S.71, F.72, Y.80 Ligands: NH4.13, NH4.18 Ligand excluded by PLIP NH4.8: 4 residues within 4Å: Chain A: S.71 Ligands: IPA.2, NH4.18, NA.26 Ligand excluded by PLIP NH4.9: 1 residues within 4Å: Chain A: K.212 Ligand excluded by PLIP NH4.10: 4 residues within 4Å: Chain A: N.161, S.162, I.201, N.203 Ligand excluded by PLIP NH4.11: 6 residues within 4Å: Chain A: Y.151, E.154, P.173, A.174, L.184 Ligands: NH4.15 Ligand excluded by PLIP NH4.12: 6 residues within 4Å: Chain A: P.129, K.215, K.216, V.217, E.218 Chain B: E.127 Ligand excluded by PLIP NH4.13: 6 residues within 4Å: Chain A: K.19, V.69, S.71, Q.82 Ligands: NH4.7, NH4.18 Ligand excluded by PLIP NH4.14: 7 residues within 4Å: Chain A: R.38, R.67, F.68, K.87, E.89, D.90 Ligands: NH4.19 Ligand excluded by PLIP NH4.15: 7 residues within 4Å: Chain A: Y.151, E.154, P.155, V.156, A.174, L.184 Ligands: NH4.11 Ligand excluded by PLIP NH4.16: 5 residues within 4Å: Chain A: D.107, Y.108, W.109 Chain B: A.45 Ligands: NH4.22 Ligand excluded by PLIP NH4.17: 6 residues within 4Å: Chain A: G.44, L.45, E.46 Chain B: S.2, G.102, G.103 Ligand excluded by PLIP NH4.18: 6 residues within 4Å: Chain A: V.69, S.71 Ligands: IPA.2, NH4.7, NH4.8, NH4.13 Ligand excluded by PLIP NH4.19: 5 residues within 4Å: Chain A: R.38, E.46, G.63, F.64 Ligands: NH4.14 Ligand excluded by PLIP NH4.20: 4 residues within 4Å: Chain A: S.17, V.18, K.19, Q.82 Ligand excluded by PLIP NH4.21: 4 residues within 4Å: Chain A: A.120, S.121, K.123, L.181 Ligand excluded by PLIP NH4.22: 7 residues within 4Å: Chain A: V.2, Q.3, L.4, Y.108, W.109, G.110 Ligands: NH4.16 Ligand excluded by PLIP NH4.33: 6 residues within 4Å: Chain B: V.29, S.31, F.32, N.33, L.34 Chain C: N.1 Ligand excluded by PLIP NH4.34: 6 residues within 4Å: Chain B: Q.112, P.113, K.114, A.115, Y.144, K.175 Ligand excluded by PLIP NH4.35: 8 residues within 4Å: Chain A: F.172 Chain B: S.118, V.119, T.120, L.139, I.140, S.141 Ligands: NA.44 Ligand excluded by PLIP NH4.36: 5 residues within 4Å: Chain B: A.151, W.152, V.159, K.160, V.163 Ligand excluded by PLIP NH4.37: 5 residues within 4Å: Chain B: Q.39, H.41, E.83, D.84 Ligands: IPA.31 Ligand excluded by PLIP NH4.38: 4 residues within 4Å: Chain B: S.61, R.63, Q.81 Ligands: IPA.31 Ligand excluded by PLIP NH4.39: 7 residues within 4Å: Chain A: P.129, A.131, K.220 Chain B: P.124, S.125, S.126, E.127 Ligand excluded by PLIP NH4.40: 8 residues within 4Å: Chain A: S.101, G.103, V.104 Chain B: H.51, E.52, K.55 Chain C: P.4, N.5 Ligand excluded by PLIP NH4.41: 3 residues within 4Å: Chain B: S.172, N.173, N.174 Ligand excluded by PLIP NH4.42: 3 residues within 4Å: Chain B: S.126, E.127, Q.130 Ligand excluded by PLIP

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

NA.23: 3 residues within 4Å: Chain A: S.9, L.114 Ligands: IPA.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.10, A:L.114 NA.24: 4 residues within 4Å: Chain A: S.126, F.128, K.149 Chain B: K.133 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.149 NA.25: 5 residues within 4Å: Chain A: E.46, A.61, P.62, F.64 Ligands: NA.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.62 NA.26: 5 residues within 4Å: Chain A: I.51, G.56, P.58 Ligands: IPA.2, NH4.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.56 NA.27: 3 residues within 4Å: Chain A: P.14, G.15, A.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.14 NA.28: 3 residues within 4Å: Chain A: A.61, P.62 Ligands: NA.25 No protein-ligand interaction detected (PLIP) NA.29: 5 residues within 4Å: Chain A: N.203, V.204, K.212, V.213, D.214 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.213, A:V.213 NA.43: 1 residues within 4Å: Chain B: K.160 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.160 NA.44: 4 residues within 4Å: Chain B: S.118, V.119, T.120 Ligands: NH4.35 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.119, B:T.120 NA.45: 3 residues within 4Å: Chain B: P.57, S.58 Ligands: NA.46 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.58 NA.46: 5 residues within 4Å: Chain A: V.104 Chain B: H.51, P.57 Ligands: IPA.5, NA.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.51 NA.47: 3 residues within 4Å: Chain B: A.82, E.85, V.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.85 NA.48: 6 residues within 4Å: Chain A: Y.95 Chain B: H.40, H.41, P.42, G.43, K.44 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.43 Water bridges: B:H.40, A:Q.39, A:Q.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kisalu, N.K. et al., A human monoclonal antibody prevents malaria infection by targeting a new site of vulnerability on the parasite. Nat. Med. (2018)

Release Date

2018-03-21

Peptides

CIS42 Fab Heavy chain: A
CIS42 Fab Light chain: B
pfCSP peptide 25: ASN-VAL-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP-PRO-ASN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

CIS42 Fab Heavy chain

CIS42 Fab Light chain

pfCSP peptide 25: ASN-VAL-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP-PRO-ASN

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