SMTL ID : 6eup.1

Crystal structure of Neisseria meningitidis NadA variant 3 double mutant A33I-I38L

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 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

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

EDO.2: 3 residues within 4Å: Chain A: D.110, L.113 Ligands: EDO.6 Ligand excluded by PLIP EDO.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: N.26, G.27, F.28, K.29, E.32 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: D.103 Chain B: K.98, D.101 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: L.113, D.114, T.117 Ligands: EDO.2, PO4.19 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: E.125, T.128, T.129, E.132 Ligand excluded by PLIP EDO.10: 1 residues within 4Å: Chain B: D.103 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain B: D.110, D.114 Ligands: EDO.26 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain B: A.131, E.132, K.135 Ligands: MPD.27 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: I.138 Chain B: T.134, N.137 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: N.126, T.129, F.130 Ligands: P6G.16 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain A: K.98 Chain C: D.103 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: T.71 Chain C: D.57, F.58 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain C: A.119, K.122, L.123, N.126 Ligands: MPD.15, MPD.27 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain C: K.135 Ligands: MPD.8, MPD.9 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: I.138 Chain C: F.130, E.133, T.134, N.137 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: T.96 Chain C: E.91, K.94, K.98 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain C: D.108, A.111 Ligands: EDO.11 Ligand excluded by PLIP

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

MPD.8: 8 residues within 4Å: Chain A: F.130, E.133, T.134, N.137 Chain C: K.135, I.138, V.139 Ligands: EDO.23 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:F.130, A:E.133, C:K.135, C:I.138, C:I.138, C:V.139 MPD.9: 5 residues within 4Å: Chain A: N.126 Chain C: T.128, A.131 Ligands: EDO.23, MPD.28 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:N.126, C:A.131 Hydrogen bonds: A:N.126 MPD.15: 4 residues within 4Å: Chain B: N.121, G.124, E.125 Ligands: EDO.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.125 MPD.27: 6 residues within 4Å: Chain B: T.128 Chain C: L.123, N.126, I.127 Ligands: EDO.12, EDO.22 No protein-ligand interaction detected (PLIP) MPD.28: 6 residues within 4Å: Chain A: A.119 Chain C: L.120, N.121, G.124, E.125 Ligands: MPD.9 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:A.119, C:L.120, C:E.125 Water bridges: A:A.119

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.16: 10 residues within 4Å: Chain A: N.121, G.124, E.125, T.128 Chain B: A.119, K.122, L.123, N.126 Ligands: EDO.14, P6G.17 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.126, A:T.128 P6G.17: 8 residues within 4Å: Chain B: D.108, A.111, A.112, D.114, A.115, N.118, A.119 Ligands: P6G.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.108, B:N.118, B:A.119

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

PO4.18: 3 residues within 4Å: Chain B: T.117, N.121 Chain C: A.119 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.121, B:N.121 PO4.19: 6 residues within 4Å: Chain A: T.117, L.120, N.121 Chain B: T.116, A.119 Ligands: EDO.6 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.121, A:N.121 Water bridges: B:T.116 PO4.29: 4 residues within 4Å: Chain A: A.119 Chain C: T.117, L.120, N.121 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Water bridges: A:A.112, A:T.116, A:A.119 Hydrogen bonds: C:N.121, C:N.121

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 A: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Adhesin A