SMTL ID : 6eun.1

Crystal structure of Neisseria meningitidis vaccine antigen NadA variant 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-trimer

Ligands

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

CL.1: 6 residues within 4Å: Chain A: A.18, N.21 Chain B: A.18, N.21 Chain C: A.18, N.21 Ligand excluded by PLIP

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

EDO.2: 2 residues within 4Å: Chain A: Q.23, E.24 No protein-ligand interaction detected (PLIP) EDO.3: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:D.110, B:T.109 EDO.11: 5 residues within 4Å: Chain B: A.131, E.132, K.135 Chain C: F.130 Ligands: P4G.21 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain B: K.98, D.101, T.102 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.98, B:T.102 EDO.13: 3 residues within 4Å: Chain B: N.20, F.28, D.56 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.20, B:D.56 EDO.14: 4 residues within 4Å: Chain B: D.103 Chain C: K.98, D.101, T.102 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.101 EDO.15: 2 residues within 4Å: Chain B: D.108, A.111 No protein-ligand interaction detected (PLIP) EDO.16: 4 residues within 4Å: Chain B: N.126, T.129, F.130 Ligands: 2PE.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.126, B:F.130 Water bridges: B:K.122 EDO.17: 3 residues within 4Å: Chain B: N.118, N.121, K.122 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.121, B:K.122 EDO.18: 3 residues within 4Å: Chain B: A.115, N.118, A.119 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.119 EDO.22: 1 residues within 4Å: Chain C: D.114 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.114 EDO.23: 2 residues within 4Å: Chain C: D.108, A.111 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.108 EDO.24: 5 residues within 4Å: Chain B: K.135, I.138 Chain C: F.130, T.134, N.137 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.134, C:N.137

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 3 residues within 4Å: Chain A: K.94, L.95 Chain C: T.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.94 PO4.5: 3 residues within 4Å: Chain A: T.116, A.119 Chain C: N.121 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.116 PO4.19: 4 residues within 4Å: Chain B: D.110, L.113, D.114 Ligands: PEG.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.114, B:D.114 PO4.25: 5 residues within 4Å: Chain B: T.117, N.121 Chain C: T.116, A.119 Ligands: MPD.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.121, B:N.121

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.6: 7 residues within 4Å: Chain A: T.117, L.120, N.121 Chain B: A.112, T.116, A.119 Ligands: 2PE.7 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.117 Hydrogen bonds: A:N.121, B:T.116, B:T.116

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.7: 13 residues within 4Å: Chain A: N.121, G.124, E.125, T.128, A.131, E.132, K.135 Chain B: A.119, K.122, L.123, N.126 Ligands: CIT.6, EDO.16 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.121, A:E.132, B:L.123, B:N.126

2 x P4G: 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE(Non-covalent)

P4G.8: 5 residues within 4Å: Chain A: L.123, N.126, F.130 Chain C: T.128 Ligands: MPD.26 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.130 Hydrogen bonds: A:N.126 P4G.21: 6 residues within 4Å: Chain B: I.127, T.128 Chain C: L.123, N.126 Ligands: EDO.11, MPD.20 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.126

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

PEG.9: 3 residues within 4Å: Chain A: E.133, T.136, N.137 No protein-ligand interaction detected (PLIP) PEG.10: 4 residues within 4Å: Chain A: A.115, N.118, A.119, K.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.119 PEG.27: 6 residues within 4Å: Chain B: D.114, T.117, N.118 Chain C: A.112, T.116 Ligands: PO4.19 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.118, C:A.112

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.20: 5 residues within 4Å: Chain B: L.120, N.121, G.124 Ligands: P4G.21, PO4.25 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.120 Hydrogen bonds: B:N.121 Water bridges: B:E.125 MPD.26: 6 residues within 4Å: Chain A: L.123 Chain C: L.120, N.121, G.124, E.125 Ligands: P4G.8 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.120, A:L.123 Water bridges: A:A.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liguori, A. et al., NadA3 Structures Reveal Undecad Coiled Coils and LOX1 Binding Regions Competed by Meningococcus B Vaccine-Elicited Human Antibodies. MBio (2018)

Release Date

2018-10-10

Peptides

Adhesin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Adhesin