SMTL ID : 6r2l.1

NYBR1-A2-SLSKILDTV

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x SER- LEU- SER- LYS- ILE- LEU- ASP- THR- VAL: SER-LEU-SER-LYS-ILE-LEU-ASP-THR-VAL(Non-covalent)

SER-LEU-SER-LYS-ILE-LEU-ASP-THR-VAL.1: 34 residues within 4Å: Chain A: M.5, Y.7, F.9, M.45, E.63, K.66, V.67, A.69, H.70, T.73, V.76, D.77, L.81, Y.84, Y.99, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, W.167, Y.171 Chain C: N.31, N.93, D.94, T.97, D.98 Chain D: W.51, S.99, I.100, S.101, S.102 34 PLIP interactions: 26 interactions with chain A, 5 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: A:Y.7, A:F.9, A:V.67, A:A.69, A:L.81, A:T.143, A:V.152, A:Q.155, A:L.156, A:Y.159, D:W.51 Hydrogen bonds: A:Y.7, A:E.63, A:K.66, A:D.77, A:Y.99, A:Y.99, A:Y.171, A:Y.171, D:I.100, D:S.102, C:N.93, C:N.93, C:D.94 Water bridges: A:E.63, A:K.66, A:D.77, A:T.80, A:R.97, A:R.97, A:W.167, D:I.100, D:Y.103 Salt bridges: A:K.146

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: E.55, G.56, P.57, E.58, R.170 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.56, A:E.58, A:Y.59, A:R.170

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

EDO.3: 7 residues within 4Å: Chain A: E.161, G.162, V.165, E.166 Chain C: A.66, T.67, R.69 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:R.169 Hydrogen bonds: C:R.69 EDO.4: 3 residues within 4Å: Chain A: E.166, R.170 Chain C: M.1 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:M.1, C:M.1, A:E.166

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: Q.87, S.88, G.91, H.93 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.88, A:S.88, A:G.91 Water bridges: A:S.88 GOL.6: 4 residues within 4Å: Chain A: S.2, G.104, S.105, L.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.2, A:S.105, A:S.105 GOL.15: 4 residues within 4Å: Chain D: E.127, V.128, V.238, S.239 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.128, D:S.239 Water bridges: D:E.127

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 5 residues within 4Å: Chain A: K.127, W.133, T.134, A.135, K.144 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.135 Water bridges: A:K.144 Salt bridges: A:K.127, A:K.144 SO4.8: 5 residues within 4Å: Chain A: F.8, Y.27, D.29, D.30 Chain B: Y.64 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.64, A:D.30 Water bridges: A:S.4 SO4.9: 3 residues within 4Å: Chain A: K.127, E.128, D.129 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.128, A:D.129, A:D.129 Water bridges: A:R.131, A:R.131 SO4.10: 4 residues within 4Å: Chain A: S.2, H.3, S.4, D.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.4 Water bridges: A:R.6 SO4.12: 8 residues within 4Å: Chain A: W.204, L.206, R.234, Q.242 Chain B: S.12, R.13, H.14, P.15 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.12, B:S.12, A:R.234, A:Q.242 Water bridges: B:A.16, B:M.100 SO4.13: 3 residues within 4Å: Chain B: S.34, D.35, I.36 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.36, B:I.36 SO4.14: 7 residues within 4Å: Chain C: Q.15, F.111, P.112, I.114, D.141, S.142, Q.143 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.15, C:P.112, C:I.114, C:D.141, C:S.142, C:Q.143 SO4.16: 5 residues within 4Å: Chain C: W.41 Chain D: V.158, E.159, L.160, T.175 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.160, D:L.160 Water bridges: D:V.158

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

EPE.11: 2 residues within 4Å: Chain B: Q.3, V.86 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rizkallah, P.J. et al., NYBR1-A2-SLSKILDTV. To Be Published

Release Date

2020-02-26

Peptides

HLA class I histocompatibility antigen, A-2 alpha chain: A
Beta-2-microglobulin: B
T cell receptor alpha variable 22,Human nkt tcr alpha chain: C
T cell receptor beta variable 11-2,Human nkt tcr beta chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

HLA class I histocompatibility antigen, A-2 alpha chain

Beta-2-microglobulin

T cell receptor alpha variable 22,Human nkt tcr alpha chain

T cell receptor beta variable 11-2,Human nkt tcr beta chain

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