SMTL ID : 8xud.1

Crystal structure of adaptor NlpI in complex with endopeptidase MepS and PDZ-protease Prc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.49 Å

Oligo State

hetero-2-2-4-mer

Ligands

2 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: Substrate peptide(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 10 residues within 4Å: Chain C: G.397, G.398, L.400, A.452, V.480, Q.481, Q.482, Y.483, R.484, S.485 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:A.452, C:Y.483 Hydrogen bonds: C:L.400, C:Q.481, C:Q.481, C:Q.481, C:Y.483, C:Y.483, C:S.485 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.2: 10 residues within 4Å: Chain D: R.220, G.397, G.398, A.399, L.400, A.452, A.453, Q.481, Q.482, Y.483 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:A.452 Hydrogen bonds: D:L.400, D:A.452, D:A.453, D:Q.481, D:Q.481, D:Q.481, D:Y.483, D:Y.483, D:Y.483

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

PO4.3: 3 residues within 4Å: Chain E: A.113, Y.147, R.151 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.147 Salt bridges: E:R.151 PO4.4: 4 residues within 4Å: Chain E: S.87, T.88, Y.89, T.116 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.88, E:T.88, E:Y.89, E:T.116 PO4.5: 4 residues within 4Å: Chain E: W.51, T.62, K.63, R.74 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.62, E:K.63 Salt bridges: E:R.74 PO4.6: 3 residues within 4Å: Chain E: R.104, R.157, S.162 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.162 Salt bridges: E:R.104, E:R.157 PO4.7: 4 residues within 4Å: Chain F: A.113, G.114, Y.147, R.151 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.114, F:Y.147 Salt bridges: F:R.151 PO4.8: 5 residues within 4Å: Chain F: S.87, T.88, Y.89, T.116, R.118 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:T.88, F:T.88, F:Y.89, F:T.116, F:T.116 Salt bridges: F:R.118 PO4.9: 3 residues within 4Å: Chain A: Y.134 Chain F: H.165, H.167 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:H.163, F:H.167 Salt bridges: F:H.167 PO4.10: 3 residues within 4Å: Chain G: R.112, A.113, Y.147 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:A.113, G:A.113 PO4.11: 5 residues within 4Å: Chain G: S.87, T.88, Y.89, T.116, R.118 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:T.88, G:T.88, G:T.88, G:Y.89, G:T.116 Salt bridges: G:R.118 PO4.12: 2 residues within 4Å: Chain G: R.104, R.157 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.157 Salt bridges: G:R.104 PO4.13: 3 residues within 4Å: Chain G: K.96, S.97, R.156 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.97 Salt bridges: G:R.156 PO4.14: 3 residues within 4Å: Chain G: T.62, K.63, R.74 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:T.62, G:K.63 Salt bridges: G:R.74 PO4.15: 4 residues within 4Å: Chain H: A.113, G.114, Y.147, R.151 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:G.114, H:Y.147, H:Y.147 Salt bridges: H:R.151 PO4.16: 4 residues within 4Å: Chain H: S.87, T.88, Y.89, T.116 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:T.88, H:T.88, H:T.88, H:Y.89, H:T.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, S. et al., Structural basis for recruitment of peptidoglycan endopeptidase MepS by lipoprotein NlpI. Nat Commun (2024)

Release Date

2024-06-05

Peptides

Lipoprotein NlpI: AB
Tail-specific protease: CD
Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
I

F
J

G
K

H
L

Lipoprotein NlpI

Tail-specific protease

Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase

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