SMTL ID : 1g1s.1

P-SELECTIN LECTIN/EGF DOMAINS COMPLEXED WITH PSGL-1 PEPTIDE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NGA- NAG- GAL- SIA- FUC- GAL: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-[beta-D-galactopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-galactopyranose

NGA-NAG-GAL-SIA-FUC-GAL.1: 18 residues within 4Å: Chain B: Y.48, E.80, N.82, K.84, R.85, E.88, E.92, Y.94, S.97, P.98, S.99, N.105, D.106, E.107 Chain C: Y.10, T.16, E.17 Ligands: SR.6 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.82, B:N.105, B:N.105, B:E.107, C:T.16, B:Y.48, B:S.97, B:S.99, B:S.99 Water bridges: B:E.88, B:R.85, B:R.85 Hydrophobic interactions: B:K.84, C:T.16 NGA-NAG-GAL-SIA-FUC-GAL.2: 19 residues within 4Å: Chain A: Y.48, E.80, N.82, K.84, R.85, E.88, E.92, Y.94, P.98, S.99, N.105, D.106, E.107, K.113 Chain D: Y.10, T.16, E.17, P.18 Ligands: SR.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.82, A:N.105, A:N.105, A:E.107, A:E.107, D:T.16, A:Y.48, A:S.99, A:S.99 Hydrophobic interactions: A:K.84, A:R.85, D:T.16 Water bridges: A:R.85, A:R.85, A:Y.44, A:Y.48, A:S.97

2 x SR: STRONTIUM ION(Non-functional Binders)

SR.3: 6 residues within 4Å: Chain A: E.80, N.82, E.88, N.105, D.106 Ligands: NGA-NAG-GAL-SIA-FUC-GAL.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.80, A:E.88, A:D.106, A:D.106 SR.6: 6 residues within 4Å: Chain B: E.80, N.82, E.88, N.105, D.106 Ligands: NGA-NAG-GAL-SIA-FUC-GAL.1 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.80, B:E.88, B:D.106, B:D.106

7 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.4: 4 residues within 4Å: Chain A: W.1, A.28, E.34, Y.118 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.1, A:W.1, A:A.28, A:Y.118, A:Y.118 Hydrogen bonds: A:A.28, A:A.28 MRD.5: 5 residues within 4Å: Chain A: N.139, Y.140, P.151, E.152 Chain B: K.66 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.140, A:P.151 Hydrogen bonds: A:N.139, A:E.152, B:K.66 Water bridges: A:T.141, A:T.141 MRD.8: 6 residues within 4Å: Chain B: W.1, Y.3, V.27, A.28, Q.30, Y.118 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.3, B:A.28, B:Y.118, B:Y.118 Hydrogen bonds: B:A.28, B:A.28 MRD.9: 4 residues within 4Å: Chain B: Y.3, Y.37, V.41, L.42 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.42 Hydrogen bonds: B:Y.3 Water bridges: B:Y.37, B:Y.37 MRD.10: 5 residues within 4Å: Chain B: W.1, Q.30, N.31, E.34, I.137 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.137 Hydrogen bonds: B:Q.30, B:N.31, B:E.34, B:E.34 Water bridges: B:I.137 MRD.11: 4 residues within 4Å: Chain B: E.132, S.143, C.144, Y.145 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.132, B:E.132, B:S.143 MRD.12: 5 residues within 4Å: Chain B: Y.10, I.14, K.17, Y.18, N.21 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.10, B:I.14, B:K.17, B:N.21 Hydrogen bonds: B:Y.10, B:N.21

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

NA.7: 1 residues within 4Å: Chain B: K.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.112 NA.13: 2 residues within 4Å: Chain C: D.9, D.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.11, C:D.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Somers, W.S. et al., Insights into the molecular basis of leukocyte tethering and rolling revealed by structures of P- and E-selectin bound to SLe(X) and PSGL-1. Cell(Cambridge,Mass.) (2000)

Release Date

2001-10-13

Peptides

P-SELECTIN: AB
PSGL-1 PEPTIDE: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

P-SELECTIN

PSGL-1 PEPTIDE

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