SMTL ID : 8h63.1

Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH10 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

hetero-1-1-mer

Ligands

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 10 residues within 4Å: Chain A: F.116, E.136, S.138, S.139, Q.156, L.157, S.158, D.179 Chain B: G.26, S.27 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:S.138, A:S.139, A:L.157, B:S.27, B:S.27 Water bridges: A:E.136, A:E.136, B:L.2, B:L.2, B:S.27, B:A.28 Salt bridges: A:E.136, A:E.136, A:D.179

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

IPA.2: 7 residues within 4Å: Chain A: D.380, T.438, F.439, S.453, G.454, T.455 Chain B: D.61 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:D.61 Hydrogen bonds: A:D.380, A:T.455, A:T.455 Water bridges: A:T.455

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: S.208, D.209, I.210, T.211, D.231, I.232, G.233, T.234 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.209, A:D.209, A:I.210, A:T.211, A:D.231, A:G.233, A:T.234 Water bridges: A:D.231, A:D.231, A:D.231 GOL.7: 7 residues within 4Å: Chain A: N.225, N.248 Chain B: V.31, N.32, V.33, T.52, R.53 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:N.32, B:R.53, A:N.225, A:N.248 Water bridges: B:R.54, A:D.245, A:D.245, A:N.248, A:N.291, A:E.292

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

NA.4: 3 residues within 4Å: Chain A: D.415, T.432, E.434 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.415, A:T.432 NA.5: 2 residues within 4Å: Chain A: S.321, S.324 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.321 NA.6: 1 residues within 4Å: Chain A: E.421 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.421, A:E.421

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamazaki, T. et al., Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes. J.Biol.Chem. (2023)

Release Date

2023-10-04

Peptides

Internalin A: A
VHH10: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Internalin A

VHH10

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