SMTL ID : 7sgr.1

Structure of hemolysin A secretion system HlyB/D complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

37 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)(Non-functional Binders)

6OU.1: 6 residues within 4Å: Chain A: I.147, F.154, I.155, L.158 Chain H: W.19, W.23 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain H Hydrophobic interactions: A:I.147, A:I.147, A:I.147, A:F.154, A:F.154, A:I.155, A:L.158, H:W.19, H:W.23 6OU.2: 8 residues within 4Å: Chain A: L.276, A.305, S.308, S.312, V.424, L.427, W.431, Q.435 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.276, A:A.305, A:V.424, A:L.427, A:W.431 6OU.3: 3 residues within 4Å: Chain A: I.207 Chain H: V.60 Ligands: 6OU.35 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:V.60 6OU.4: 3 residues within 4Å: Chain A: N.192 Chain B: W.394 Ligands: 6OU.5 No protein-ligand interaction detected (PLIP) 6OU.5: 5 residues within 4Å: Chain A: S.199, V.203 Chain B: T.387, W.394 Ligands: 6OU.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.203, B:T.387, B:W.394 6OU.6: 2 residues within 4Å: Chain A: K.181, V.193 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.181 6OU.7: 9 residues within 4Å: Chain B: I.147, R.151, F.154, L.158, F.216, L.270 Ligands: 6OU.11, 6OU.14, 6OU.19 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.147, B:R.151, B:F.154, B:L.158, B:L.270 6OU.8: 3 residues within 4Å: Chain B: K.292, I.391, L.395 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.391, B:L.395 6OU.9: 12 residues within 4Å: Chain B: I.314, R.317, R.318 Chain E: F.143, I.147, I.148, R.151, F.154, L.158, F.216, I.223 Ligands: 6OU.28 15 PLIP interactions: 11 interactions with chain E, 4 interactions with chain B Hydrophobic interactions: E:F.143, E:I.147, E:I.148, E:R.151, E:F.154, E:F.154, E:L.158, E:F.216, E:F.216, E:I.223 Salt bridges: E:R.151, B:R.318, B:R.318, B:K.369 Hydrogen bonds: B:R.317 6OU.10: 1 residues within 4Å: Ligands: 6OU.35 No protein-ligand interaction detected (PLIP) 6OU.11: 3 residues within 4Å: Chain B: R.151 Ligands: 6OU.7, 6OU.20 No protein-ligand interaction detected (PLIP) 6OU.12: 3 residues within 4Å: Chain B: V.296, F.299, C.303 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.296, B:F.299 6OU.13: 4 residues within 4Å: Chain B: F.140, R.316, F.434, G.438 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.140, B:F.140, B:F.434 6OU.14: 7 residues within 4Å: Chain B: F.140, F.143, I.144, I.147, F.264, L.265 Ligands: 6OU.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.140, B:F.140, B:F.143, B:I.144, B:I.147, B:F.264, B:L.265 6OU.15: 2 residues within 4Å: Chain B: A.306, V.309 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.306, B:V.309 6OU.16: 11 residues within 4Å: Chain B: W.287 Chain C: K.292, L.295, V.296, F.299, C.303, T.387, I.391, L.395 Ligands: 6OU.22, 6OU.24 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.296, C:T.387, C:I.391 Salt bridges: C:K.292 Hydrogen bonds: B:W.287 6OU.17: 8 residues within 4Å: Chain C: W.307, Q.379, L.383, I.384 Chain D: G.210, L.211, Y.214 Ligands: 6OU.20 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:W.307, C:W.307, C:Q.379, C:L.383, C:I.384, D:L.211, D:Y.214 6OU.18: 9 residues within 4Å: Chain C: W.287, Y.288 Chain E: K.292, F.299, T.387, V.388, I.391, W.394, L.395 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:F.299, E:T.387, E:V.388, E:I.391, E:W.394, E:W.394, C:Y.288 Salt bridges: E:K.292 6OU.19: 7 residues within 4Å: Chain B: I.144, I.148 Chain C: F.310, R.318, L.373 Ligands: 6OU.7, 6OU.20 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.373 Hydrogen bonds: C:R.318, C:R.318 Salt bridges: C:R.318 6OU.20: 3 residues within 4Å: Ligands: 6OU.11, 6OU.17, 6OU.19 No protein-ligand interaction detected (PLIP) 6OU.21: 3 residues within 4Å: Chain C: A.306, W.307, V.309 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.306, C:W.307 6OU.22: 7 residues within 4Å: Chain B: L.295 Chain C: W.287, P.291, K.292, L.295 Chain E: L.295 Ligands: 6OU.16 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.295, B:L.295 Hydrogen bonds: C:K.292 6OU.23: 6 residues within 4Å: Chain C: G.210 Chain D: W.307, Q.379, G.380, L.383, I.384 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.307, D:Q.379, D:L.383, D:I.384 6OU.24: 7 residues within 4Å: Chain C: T.387, I.390, W.394 Chain D: T.195, S.199, V.203 Ligands: 6OU.16 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:T.195, D:V.203, C:T.387, C:I.390, C:W.394 6OU.25: 1 residues within 4Å: Chain E: W.287 No protein-ligand interaction detected (PLIP) 6OU.26: 1 residues within 4Å: Ligands: 6OU.33 No protein-ligand interaction detected (PLIP) 6OU.27: 3 residues within 4Å: Chain C: V.273 Chain E: F.310, P.313 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:F.310, E:P.313, C:V.273 6OU.28: 5 residues within 4Å: Chain E: F.140, T.141, F.143, I.144 Ligands: 6OU.9 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.140, E:T.141, E:F.143, E:F.143, E:I.144 6OU.29: 11 residues within 4Å: Chain F: F.140, I.144, I.147, R.151, F.154, I.155, F.216, F.264, L.265, L.270 Chain G: Y.15 10 PLIP interactions: 9 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:I.144, F:I.144, F:I.147, F:R.151, F:F.154, F:F.154, F:I.155, F:F.216, F:L.270, G:Y.15 6OU.30: 5 residues within 4Å: Chain F: S.308, S.312, V.424, L.427, W.431 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:V.424, F:L.427, F:W.431, F:W.431 6OU.31: 6 residues within 4Å: Chain E: G.210 Chain F: A.306, I.376, G.380, L.383 Chain K: R.56 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:A.306, F:I.376, F:L.383 6OU.32: 1 residues within 4Å: Chain F: K.181 No protein-ligand interaction detected (PLIP) 6OU.33: 12 residues within 4Å: Chain E: W.307, I.376, Q.379, G.380, L.383 Chain F: G.210, L.211, Y.214 Chain G: S.54, R.56, P.57 Ligands: 6OU.26 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain G Hydrophobic interactions: E:W.307, E:I.376, E:Q.379 Hydrogen bonds: G:S.54, G:S.54 6OU.34: 4 residues within 4Å: Chain F: A.197, V.201 Chain G: A.71, S.75 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:A.197, F:V.201, G:A.71 6OU.35: 9 residues within 4Å: Chain A: G.210, L.211, Y.214 Chain B: W.307, Q.379, L.383 Chain H: S.54 Ligands: 6OU.3, 6OU.10 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.307, B:Q.379, B:L.383, A:L.211, A:Y.214 6OU.36: 2 residues within 4Å: Chain A: V.201 Chain H: S.75 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.201 6OU.37: 10 residues within 4Å: Chain A: W.307, F.310, I.376, Q.379, G.380, L.383 Chain B: G.210, L.211, Y.214 Chain L: R.56 10 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B, 2 interactions with chain L Hydrophobic interactions: A:W.307, A:W.307, A:F.310, A:I.376, A:I.376, A:L.383 Hydrogen bonds: B:Y.214, B:Y.214 Salt bridges: L:R.56, L:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, H. et al., The hemolysin A secretion system is a multi-engine pump containing three ABC transporters. Cell (2022)

Release Date

2022-09-14

Peptides

Alpha-hemolysin translocation ATP-binding protein HlyB: ABCDEF
Membrane fusion protein (MFP) family protein,Hemolysin secretion protein D, chromosomal: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
I

C
A

D
B

E
E

F
F

G
H

H
L

I
D

J
C

K
G

L
K

Membrane

We predict this structure to be a membrane protein.
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Alpha-hemolysin translocation ATP-binding protein HlyB

Membrane fusion protein (MFP) family protein,Hemolysin secretion protein D, chromosomal